scte-quant 1.3.3__tar.gz

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  1. scte_quant-1.3.3/.gitignore +8 -0
  2. scte_quant-1.3.3/AGENTS.md +259 -0
  3. scte_quant-1.3.3/Data/Gene.gtf +100 -0
  4. scte_quant-1.3.3/Data/TE.bed +102 -0
  5. scte_quant-1.3.3/Data/test.bam +0 -0
  6. scte_quant-1.3.3/LICENSE +21 -0
  7. scte_quant-1.3.3/PKG-INFO +276 -0
  8. scte_quant-1.3.3/README.md +248 -0
  9. scte_quant-1.3.3/bin/scTE +177 -0
  10. scte_quant-1.3.3/bin/scTEATAC +219 -0
  11. scte_quant-1.3.3/bin/scTEATAC_build +89 -0
  12. scte_quant-1.3.3/bin/scTE_build +693 -0
  13. scte_quant-1.3.3/build.sh +3 -0
  14. scte_quant-1.3.3/docs/scTE.png +0 -0
  15. scte_quant-1.3.3/example/Figure3/0.cluster_scripts/scte/do_batch.sh +17 -0
  16. scte_quant-1.3.3/example/Figure3/0.cluster_scripts/scte/scte.sh +13 -0
  17. scte_quant-1.3.3/example/Figure3/0.cluster_scripts/starsolo/do_batch.sh +18 -0
  18. scte_quant-1.3.3/example/Figure3/0.cluster_scripts/starsolo/starsolo.sh +32 -0
  19. scte_quant-1.3.3/example/Figure3/1.pack.py +135 -0
  20. scte_quant-1.3.3/example/Figure3/2.norm_and_learn.py +51 -0
  21. scte_quant-1.3.3/example/Figure3/3.diffexp.py +83 -0
  22. scte_quant-1.3.3/example/Figure3/4.plots-allgenes.py +30 -0
  23. scte_quant-1.3.3/example/Figure3/4.plots-alltes.py +31 -0
  24. scte_quant-1.3.3/example/Figure3/4.plots-specific-tes.py +45 -0
  25. scte_quant-1.3.3/example/Figure3/5.marker_genes-leiden-0.2.py +50 -0
  26. scte_quant-1.3.3/example/Figure3/5.marker_genes-small-grp_cut.py +70 -0
  27. scte_quant-1.3.3/example/Figure3/5.marker_genes-small.py +41 -0
  28. scte_quant-1.3.3/example/Figure3/5.marker_genes.py +66 -0
  29. scte_quant-1.3.3/example/Figure3/TE_genes_id.mm10.txt.gz +0 -0
  30. scte_quant-1.3.3/meta.yaml +34 -0
  31. scte_quant-1.3.3/pyproject.toml +32 -0
  32. scte_quant-1.3.3/run_test.sh +4 -0
  33. scte_quant-1.3.3/scTE/__init__.py +11 -0
  34. scte_quant-1.3.3/scTE/_version.py +24 -0
  35. scte_quant-1.3.3/scTE/annotation.py +158 -0
  36. scte_quant-1.3.3/scTE/base.py +473 -0
  37. scte_quant-1.3.3/scTE/miniglbase/README.md +25 -0
  38. scte_quant-1.3.3/scTE/miniglbase/__init__.py +54 -0
  39. scte_quant-1.3.3/scTE/miniglbase/base_genelist.py +324 -0
  40. scte_quant-1.3.3/scTE/miniglbase/config.py +45 -0
  41. scte_quant-1.3.3/scTE/miniglbase/genelist.py +1681 -0
  42. scte_quant-1.3.3/scTE/miniglbase/location.py +249 -0
  43. scte_quant-1.3.3/scTE/miniglbase/utils.py +59 -0
  44. scte_quant-1.3.3/scTE/scatacseq.py +293 -0
  45. scte_quant-1.3.3/scte_quant.egg-info/PKG-INFO +276 -0
  46. scte_quant-1.3.3/scte_quant.egg-info/SOURCES.txt +50 -0
  47. scte_quant-1.3.3/scte_quant.egg-info/dependency_links.txt +1 -0
  48. scte_quant-1.3.3/scte_quant.egg-info/not-zip-safe +1 -0
  49. scte_quant-1.3.3/scte_quant.egg-info/requires.txt +5 -0
  50. scte_quant-1.3.3/scte_quant.egg-info/top_level.txt +1 -0
  51. scte_quant-1.3.3/setup.cfg +4 -0
  52. scte_quant-1.3.3/setup.py +41 -0
scte_quant-1.3.3/.gitignore ADDED
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+ build/
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+ *.egg-info/
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+ .Rproj.user/
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+ dist/
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+ .ipynb_checkpoints/
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+ *.pyc
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+ */_version.py
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+ Data/human_index/
scte_quant-1.3.3/AGENTS.md ADDED
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+ # AGENTS.md - Agentic Coding Guidelines for scTE
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+
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+ ## Project Overview
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+
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+ scTE is a Python tool for quantifying transposable element (TE) expression from single-cell RNA sequencing data. It takes BAM/SAM files along with gene (GTF) and TE (BED) annotations to produce expression matrices.
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+
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+ - **Language**: Python >= 3.9
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+ - **Package Manager**: setuptools with pyproject.toml
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+ - **Dependencies**: scipy, pandas, numpy, anndata, h5py==3.1.0
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+
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+ ---
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+
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+ ## Build, Lint, and Test Commands
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+
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+ ### Installation (Development)
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+
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+ ```bash
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+ pip install -e . # Install in editable mode
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+ pip install . # Regular install
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+ ```
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+
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+ ### Running Tests
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+
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+ There is no formal test suite. The `run_test.sh` script runs the tool with sample data:
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+
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+ ```bash
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+ ./run_test.sh # Run integration test with Data/ directory
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+ ```
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+
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+ To run a single test manually:
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+
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+ ```bash
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+ # Build index
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+ scTE_build -g mm10 -te Data/TE.bed -gene Data/Gene.gtf -o Data/test -m exclusive
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+
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+ # Run scTE
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+ scTE -i Data/test.bam -p 12 --min_genes 1 -o out -x Data/test.exclusive.idx
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+ ```
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+
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+ ### Linting
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+
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+ No formal linter is configured. Run manually:
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+
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+ ```bash
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+ flake8 scTE/ # Check Python style
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+ ruff check scTE/ # Alternative linter
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+ ```
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+
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+ ### Type Checking
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+
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+ No type checker configured. Run manually if needed:
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+
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+ ```bash
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+ mypy scTE/ # Type check (if mypy installed)
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+ ```
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+
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+ ---
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+
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+ ## Code Style Guidelines
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+
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+ ### Imports
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+
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+ Standard order (left to right, top to bottom):
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+ 1. Python standard library (`os`, `sys`, `glob`, `argparse`, `logging`, etc.)
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+ 2. Third-party packages (`pandas`, `numpy`, `scipy`, `anndata`)
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+ 3. Local project imports (`from scTE.miniglbase import ...`)
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+
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+ ```python
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+ # Good
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+ import os
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+ import sys
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+ import gzip
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+ import logging
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+ import argparse
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+ from functools import partial
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+ import pandas as pd
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+ import numpy as np
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+ import scipy
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+ import anndata as ad
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+ from scTE.miniglbase import genelist, glload, location
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+ from scTE.annotation import annoGtf
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+ ```
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+
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+ ### Naming Conventions
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+
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+ - **Functions/variables**: `snake_case` (e.g., `read_opts`, `allelement`)
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+ - **Classes**: `PascalCase` (e.g., `MyClass`) - though this project has few classes
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+ - **Constants**: `UPPER_SNAKE_CASE` (e.g., `DEFAULT_THREADS = 1`)
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+ - **Private functions**: prefix with underscore (e.g., `_internal_function`)
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+
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+ ### Type Hints
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+
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+ Not currently used in this codebase, but adding them is encouraged for new code:
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+
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+ ```python
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+ # Preferred for new code
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+ def process_bam(filename: str, threads: int = 1) -> dict:
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+ ...
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+
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+ # Current style (acceptable)
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+ def process_bam(filename, threads):
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+ ...
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+ ```
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+
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+ ### Docstrings
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+
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+ Use this format for functions (as seen in existing code):
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+
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+ ```python
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+ def splitAllChrs(chromosome_list, filename, genenumber, countnumber, UMI=True):
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+ '''
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+ **Purpose**
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+ Split the data into separate beds, and count up all the times each barcode appears
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+
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+ **Arguments**
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+ chromosome_list
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+ List of chromosome names
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+
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+ filename (Required)
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+ filename stub to use for tmp files
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+
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+ **Returns**
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+ The barcode whitelist
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+ '''
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+ ```
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+
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+ ### Error Handling
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+
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+ - Use `logging.error()` + `sys.exit(1)` for fatal errors:
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+ ```python
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+ logging.error("The input file %s has no cell barcodes information" % filename)
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+ sys.exit(1)
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+ ```
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+
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+ - Use `logging.warning()` for non-fatal issues
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+ - Use `logging.info()` for progress messages
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+ - Assert Python version requirements:
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+ ```python
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+ assert sys.version_info >= (3, 6), 'Python >=3.6 is required'
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+ ```
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+
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+ ### File Handling
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+
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+ - Use `gzip.open()` for compressed files with `'rt'` or `'wt'` mode for text
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+ - Use context managers (`with` statement) where possible
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+ - Close file handles explicitly when not using context managers
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+
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+ ```python
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+ # Good
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+ with gzip.open('output.bed.gz', 'wt') as oh:
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+ oh.write(line)
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+
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+ # Also acceptable
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+ oh = gzip.open('output.bed.gz', 'wt')
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+ # ... process ...
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+ oh.close()
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+ ```
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+
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+ ### CLI Interface
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+
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+ Use `argparse` with this structure:
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+
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+ ```python
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+ def prepare_parser():
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+ desc = "Tool description"
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+ exmp = "Example: tool <-i input> <-o output>"
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+ parser = argparse.ArgumentParser(prog='scTE', description=desc, epilog=exmp)
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+
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+ optional = parser._action_groups.pop()
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+ optional.add_argument('--option', dest='option', type=int, default=200, help='Help text')
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+
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+ required = parser.add_argument_group('required arguments')
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+ required.add_argument('-i', '--input', dest='input', required=True, help='Input file')
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+
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+ parser._action_groups.append(optional)
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+ return parser
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+ ```
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+
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+ ### Logging Setup
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+
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+ Configure logging at module level:
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+
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+ ```python
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+ import logging
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+ logging.getLogger("zarr").setLevel(logging.WARNING)
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+ ```
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+
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+ Add logger methods to args object:
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+
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+ ```python
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+ args.error = logging.critical
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+ args.warn = logging.warning
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+ args.debug = logging.debug
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+ args.info = logging.info
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+ ```
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+
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+ ### Performance Considerations
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+
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+ - Use `defaultdict(int)` for counting
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+ - Use list comprehensions where appropriate
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+ - Consider memory usage with large files (streaming where possible)
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+ - Use multiprocessing for parallel operations
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+
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+ ### Shell Commands
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+
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+ Use `subprocess.run()` with `shell=True` for external commands, or `os.system()` for simple cases:
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+
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+ ```python
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+ # With subprocess
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+ subprocess.run('samtools view %s | head -100' % filename, shell=True)
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+
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+ # With os.system
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+ os.system('mkdir -p %s_scTEtmp/o1' % out)
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+ ```
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+
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+ ### Code to Avoid
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+
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+ - Avoid leaving large blocks of commented-out code
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+ - Avoid using `from module import *`
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+ - Avoid bare `except:` clauses - use specific exceptions
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+ - Avoid trailing whitespace
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+
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+ ---
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+
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+ ## Project Structure
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+
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+ ```
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+ scTE/
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+ ├── bin/ # CLI entry points (scTE, scTE_build, etc.)
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+ ├── scTE/
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+ │ ├── __init__.py # Package init, version
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+ │ ├── base.py # Core processing functions
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+ │ ├── annotation.py # GTF/BED annotation handling
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+ │ ├── scatacseq.py # scATAC-seq functionality
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+ │ └── miniglbase/ # Internal genome index library
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+ ├── Data/ # Test data
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+ ├── setup.py # Package configuration
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+ └── pyproject.toml # Build system config
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+ ```
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+
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+ ---
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+
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+ ## Common Tasks
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+
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+ ### Adding a new CLI argument
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+
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+ 1. Add to `prepare_parser()` in `bin/scTE`
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+ 2. Add handling in `read_opts()` in `scTE/base.py`
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+ 3. Add to argument validation if needed
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+
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+ ### Modifying the index format
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+
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+ Changes may require updates to `scTE/miniglbase/` - the genelist and location classes handle genome coordinate indexing.
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+
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+ ### Adding dependencies
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+
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+ Update both:
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+ - `pyproject.toml` under `[project].dependencies`
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+ - `meta.yaml` (for conda)
scte_quant-1.3.3/Data/Gene.gtf ADDED
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+ ##description: evidence-based annotation of the mouse genome (GRCm38), version M21 (Ensembl 96)
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+ ##provider: GENCODE
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+ ##contact: gencode-help@ebi.ac.uk
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+ ##format: gtf
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+ ##date: 2019-03-27
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+ chr1 HAVANA gene 3073253 3074322 . + . gene_id "ENSMUSG00000102693.1"; gene_type "TEC"; gene_name "4933401J01Rik"; level 2; havana_gene "OTTMUSG00000049935.1";
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+ chr1 HAVANA transcript 3073253 3074322 . + . gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_name "4933401J01Rik"; transcript_type "TEC"; transcript_name "4933401J01Rik-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049935.1"; havana_transcript "OTTMUST00000127109.1";
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+ chr1 HAVANA exon 3073253 3074322 . + . gene_id "ENSMUSG00000102693.1"; transcript_id "ENSMUST00000193812.1"; gene_type "TEC"; gene_name "4933401J01Rik"; transcript_type "TEC"; transcript_name "4933401J01Rik-201"; exon_number 1; exon_id "ENSMUSE00001343744.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049935.1"; havana_transcript "OTTMUST00000127109.1";
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+ chr1 ENSEMBL gene 3102016 3102125 . + . gene_id "ENSMUSG00000064842.1"; gene_type "snRNA"; gene_name "Gm26206"; level 3;
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+ chr1 ENSEMBL transcript 3102016 3102125 . + . gene_id "ENSMUSG00000064842.1"; transcript_id "ENSMUST00000082908.1"; gene_type "snRNA"; gene_name "Gm26206"; transcript_type "snRNA"; transcript_name "Gm26206-201"; level 3; transcript_support_level "NA"; tag "basic";
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+ chr1 ENSEMBL exon 3102016 3102125 . + . gene_id "ENSMUSG00000064842.1"; transcript_id "ENSMUST00000082908.1"; gene_type "snRNA"; gene_name "Gm26206"; transcript_type "snRNA"; transcript_name "Gm26206-201"; exon_number 1; exon_id "ENSMUSE00000522066.1"; level 3; transcript_support_level "NA"; tag "basic";
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+ chr1 HAVANA gene 3205901 3671498 . - . gene_id "ENSMUSG00000051951.5"; gene_type "protein_coding"; gene_name "Xkr4"; level 2; havana_gene "OTTMUSG00000026353.2";
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+ chr1 HAVANA transcript 3205901 3216344 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000162897.1"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "processed_transcript"; transcript_name "Xkr4-203"; level 2; transcript_support_level "1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000086625.1";
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+ chr1 HAVANA exon 3213609 3216344 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000162897.1"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "processed_transcript"; transcript_name "Xkr4-203"; exon_number 1; exon_id "ENSMUSE00000858910.1"; level 2; transcript_support_level "1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000086625.1";
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+ chr1 HAVANA exon 3205901 3207317 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000162897.1"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "processed_transcript"; transcript_name "Xkr4-203"; exon_number 2; exon_id "ENSMUSE00000866652.1"; level 2; transcript_support_level "1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000086625.1";
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+ chr1 HAVANA transcript 3206523 3215632 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000159265.1"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "processed_transcript"; transcript_name "Xkr4-202"; level 2; transcript_support_level "1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000086624.1";
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+ chr1 HAVANA exon 3213439 3215632 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000159265.1"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "processed_transcript"; transcript_name "Xkr4-202"; exon_number 1; exon_id "ENSMUSE00000863980.1"; level 2; transcript_support_level "1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000086624.1";
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+ chr1 HAVANA exon 3206523 3207317 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000159265.1"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "processed_transcript"; transcript_name "Xkr4-202"; exon_number 2; exon_id "ENSMUSE00000867897.1"; level 2; transcript_support_level "1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000086624.1";
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+ chr1 HAVANA transcript 3214482 3671498 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
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+ chr1 HAVANA exon 3670552 3671498 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 1; exon_id "ENSMUSE00000485541.3"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
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+ chr1 HAVANA CDS 3670552 3671348 . - 0 gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 1; exon_id "ENSMUSE00000485541.3"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
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+ chr1 HAVANA start_codon 3671346 3671348 . - 0 gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 1; exon_id "ENSMUSE00000485541.3"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
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+ chr1 HAVANA exon 3421702 3421901 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 2; exon_id "ENSMUSE00000449517.3"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
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+ chr1 HAVANA CDS 3421702 3421901 . - 1 gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 2; exon_id "ENSMUSE00000449517.3"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
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+ chr1 HAVANA exon 3214482 3216968 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 3; exon_id "ENSMUSE00000448840.2"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
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+ chr1 HAVANA CDS 3216025 3216968 . - 2 gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 3; exon_id "ENSMUSE00000448840.2"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
27
+ chr1 HAVANA stop_codon 3216022 3216024 . - 0 gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 3; exon_id "ENSMUSE00000448840.2"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
28
+ chr1 HAVANA UTR 3671349 3671498 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 1; exon_id "ENSMUSE00000485541.3"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
29
+ chr1 HAVANA UTR 3214482 3216024 . - . gene_id "ENSMUSG00000051951.5"; transcript_id "ENSMUST00000070533.4"; gene_type "protein_coding"; gene_name "Xkr4"; transcript_type "protein_coding"; transcript_name "Xkr4-201"; exon_number 3; exon_id "ENSMUSE00000448840.2"; level 2; protein_id "ENSMUSP00000070648.4"; transcript_support_level "1"; tag "basic"; tag "appris_principal_1"; tag "CCDS"; ccdsid "CCDS14803.1"; havana_gene "OTTMUSG00000026353.2"; havana_transcript "OTTMUST00000065166.1";
30
+ chr1 HAVANA gene 3252757 3253236 . + . gene_id "ENSMUSG00000102851.1"; gene_type "processed_pseudogene"; gene_name "Gm18956"; level 1; tag "pseudo_consens"; havana_gene "OTTMUSG00000049958.1";
31
+ chr1 HAVANA transcript 3252757 3253236 . + . gene_id "ENSMUSG00000102851.1"; transcript_id "ENSMUST00000192857.1"; gene_type "processed_pseudogene"; gene_name "Gm18956"; transcript_type "processed_pseudogene"; transcript_name "Gm18956-201"; level 1; transcript_support_level "NA"; ont "PGO:0000004"; tag "pseudo_consens"; tag "basic"; havana_gene "OTTMUSG00000049958.1"; havana_transcript "OTTMUST00000127143.1";
32
+ chr1 HAVANA exon 3252757 3253236 . + . gene_id "ENSMUSG00000102851.1"; transcript_id "ENSMUST00000192857.1"; gene_type "processed_pseudogene"; gene_name "Gm18956"; transcript_type "processed_pseudogene"; transcript_name "Gm18956-201"; exon_number 1; exon_id "ENSMUSE00001339323.1"; level 1; transcript_support_level "NA"; ont "PGO:0000004"; tag "pseudo_consens"; tag "basic"; havana_gene "OTTMUSG00000049958.1"; havana_transcript "OTTMUST00000127143.1";
33
+ chr1 HAVANA gene 3365731 3368549 . - . gene_id "ENSMUSG00000103377.1"; gene_type "TEC"; gene_name "Gm37180"; level 2; havana_gene "OTTMUSG00000049960.1";
34
+ chr1 HAVANA transcript 3365731 3368549 . - . gene_id "ENSMUSG00000103377.1"; transcript_id "ENSMUST00000195335.1"; gene_type "TEC"; gene_name "Gm37180"; transcript_type "TEC"; transcript_name "Gm37180-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049960.1"; havana_transcript "OTTMUST00000127145.1";
35
+ chr1 HAVANA exon 3365731 3368549 . - . gene_id "ENSMUSG00000103377.1"; transcript_id "ENSMUST00000195335.1"; gene_type "TEC"; gene_name "Gm37180"; transcript_type "TEC"; transcript_name "Gm37180-201"; exon_number 1; exon_id "ENSMUSE00001343189.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049960.1"; havana_transcript "OTTMUST00000127145.1";
36
+ chr1 HAVANA gene 3375556 3377788 . - . gene_id "ENSMUSG00000104017.1"; gene_type "TEC"; gene_name "Gm37363"; level 2; havana_gene "OTTMUSG00000049961.1";
37
+ chr1 HAVANA transcript 3375556 3377788 . - . gene_id "ENSMUSG00000104017.1"; transcript_id "ENSMUST00000192336.1"; gene_type "TEC"; gene_name "Gm37363"; transcript_type "TEC"; transcript_name "Gm37363-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049961.1"; havana_transcript "OTTMUST00000127146.1";
38
+ chr1 HAVANA exon 3375556 3377788 . - . gene_id "ENSMUSG00000104017.1"; transcript_id "ENSMUST00000192336.1"; gene_type "TEC"; gene_name "Gm37363"; transcript_type "TEC"; transcript_name "Gm37363-201"; exon_number 1; exon_id "ENSMUSE00001343686.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049961.1"; havana_transcript "OTTMUST00000127146.1";
39
+ chr1 HAVANA gene 3464977 3467285 . - . gene_id "ENSMUSG00000103025.1"; gene_type "TEC"; gene_name "Gm37686"; level 2; havana_gene "OTTMUSG00000049930.1";
40
+ chr1 HAVANA transcript 3464977 3467285 . - . gene_id "ENSMUSG00000103025.1"; transcript_id "ENSMUST00000194099.1"; gene_type "TEC"; gene_name "Gm37686"; transcript_type "TEC"; transcript_name "Gm37686-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049930.1"; havana_transcript "OTTMUST00000127101.1";
41
+ chr1 HAVANA exon 3464977 3467285 . - . gene_id "ENSMUSG00000103025.1"; transcript_id "ENSMUST00000194099.1"; gene_type "TEC"; gene_name "Gm37686"; transcript_type "TEC"; transcript_name "Gm37686-201"; exon_number 1; exon_id "ENSMUSE00001337180.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049930.1"; havana_transcript "OTTMUST00000127101.1";
42
+ chr1 HAVANA gene 3466587 3513553 . + . gene_id "ENSMUSG00000089699.1"; gene_type "antisense"; gene_name "Gm1992"; level 2; havana_gene "OTTMUSG00000026352.1";
43
+ chr1 HAVANA transcript 3466587 3513553 . + . gene_id "ENSMUSG00000089699.1"; transcript_id "ENSMUST00000161581.1"; gene_type "antisense"; gene_name "Gm1992"; transcript_type "antisense"; transcript_name "Gm1992-201"; level 2; transcript_support_level "3"; tag "basic"; havana_gene "OTTMUSG00000026352.1"; havana_transcript "OTTMUST00000065165.1";
44
+ chr1 HAVANA exon 3466587 3466687 . + . gene_id "ENSMUSG00000089699.1"; transcript_id "ENSMUST00000161581.1"; gene_type "antisense"; gene_name "Gm1992"; transcript_type "antisense"; transcript_name "Gm1992-201"; exon_number 1; exon_id "ENSMUSE00000869502.1"; level 2; transcript_support_level "3"; tag "basic"; havana_gene "OTTMUSG00000026352.1"; havana_transcript "OTTMUST00000065165.1";
45
+ chr1 HAVANA exon 3513405 3513553 . + . gene_id "ENSMUSG00000089699.1"; transcript_id "ENSMUST00000161581.1"; gene_type "antisense"; gene_name "Gm1992"; transcript_type "antisense"; transcript_name "Gm1992-201"; exon_number 2; exon_id "ENSMUSE00000864479.1"; level 2; transcript_support_level "3"; tag "basic"; havana_gene "OTTMUSG00000026352.1"; havana_transcript "OTTMUST00000065165.1";
46
+ chr1 HAVANA gene 3512451 3514507 . - . gene_id "ENSMUSG00000103201.1"; gene_type "TEC"; gene_name "Gm37329"; level 2; havana_gene "OTTMUSG00000049929.1";
47
+ chr1 HAVANA transcript 3512451 3514507 . - . gene_id "ENSMUSG00000103201.1"; transcript_id "ENSMUST00000192973.1"; gene_type "TEC"; gene_name "Gm37329"; transcript_type "TEC"; transcript_name "Gm37329-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049929.1"; havana_transcript "OTTMUST00000127100.1";
48
+ chr1 HAVANA exon 3512451 3514507 . - . gene_id "ENSMUSG00000103201.1"; transcript_id "ENSMUST00000192973.1"; gene_type "TEC"; gene_name "Gm37329"; transcript_type "TEC"; transcript_name "Gm37329-201"; exon_number 1; exon_id "ENSMUSE00001345667.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049929.1"; havana_transcript "OTTMUST00000127100.1";
49
+ chr1 HAVANA gene 3531795 3532720 . + . gene_id "ENSMUSG00000103147.1"; gene_type "processed_pseudogene"; gene_name "Gm7341"; level 1; tag "pseudo_consens"; havana_gene "OTTMUSG00000049921.1";
50
+ chr1 HAVANA transcript 3531795 3532720 . + . gene_id "ENSMUSG00000103147.1"; transcript_id "ENSMUST00000192183.1"; gene_type "processed_pseudogene"; gene_name "Gm7341"; transcript_type "processed_pseudogene"; transcript_name "Gm7341-201"; level 1; transcript_support_level "NA"; ont "PGO:0000004"; tag "pseudo_consens"; tag "basic"; havana_gene "OTTMUSG00000049921.1"; havana_transcript "OTTMUST00000127089.1";
51
+ chr1 HAVANA exon 3531795 3532720 . + . gene_id "ENSMUSG00000103147.1"; transcript_id "ENSMUST00000192183.1"; gene_type "processed_pseudogene"; gene_name "Gm7341"; transcript_type "processed_pseudogene"; transcript_name "Gm7341-201"; exon_number 1; exon_id "ENSMUSE00001343235.1"; level 1; transcript_support_level "NA"; ont "PGO:0000004"; tag "pseudo_consens"; tag "basic"; havana_gene "OTTMUSG00000049921.1"; havana_transcript "OTTMUST00000127089.1";
52
+ chr1 HAVANA gene 3592892 3595903 . - . gene_id "ENSMUSG00000103161.1"; gene_type "TEC"; gene_name "Gm38148"; level 2; havana_gene "OTTMUSG00000049927.1";
53
+ chr1 HAVANA transcript 3592892 3595903 . - . gene_id "ENSMUSG00000103161.1"; transcript_id "ENSMUST00000195166.1"; gene_type "TEC"; gene_name "Gm38148"; transcript_type "TEC"; transcript_name "Gm38148-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049927.1"; havana_transcript "OTTMUST00000127098.1";
54
+ chr1 HAVANA exon 3592892 3595903 . - . gene_id "ENSMUSG00000103161.1"; transcript_id "ENSMUST00000195166.1"; gene_type "TEC"; gene_name "Gm38148"; transcript_type "TEC"; transcript_name "Gm38148-201"; exon_number 1; exon_id "ENSMUSE00001343966.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049927.1"; havana_transcript "OTTMUST00000127098.1";
55
+ chr1 HAVANA gene 3647309 3658904 . - . gene_id "ENSMUSG00000102331.1"; gene_type "sense_intronic"; gene_name "Gm19938"; level 2; havana_gene "OTTMUSG00000049924.1";
56
+ chr1 HAVANA transcript 3647309 3658904 . - . gene_id "ENSMUSG00000102331.1"; transcript_id "ENSMUST00000192692.1"; gene_type "sense_intronic"; gene_name "Gm19938"; transcript_type "sense_intronic"; transcript_name "Gm19938-201"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTMUSG00000049924.1"; havana_transcript "OTTMUST00000127092.1";
57
+ chr1 HAVANA exon 3658847 3658904 . - . gene_id "ENSMUSG00000102331.1"; transcript_id "ENSMUST00000192692.1"; gene_type "sense_intronic"; gene_name "Gm19938"; transcript_type "sense_intronic"; transcript_name "Gm19938-201"; exon_number 1; exon_id "ENSMUSE00001337496.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTMUSG00000049924.1"; havana_transcript "OTTMUST00000127092.1";
58
+ chr1 HAVANA exon 3647309 3650509 . - . gene_id "ENSMUSG00000102331.1"; transcript_id "ENSMUST00000192692.1"; gene_type "sense_intronic"; gene_name "Gm19938"; transcript_type "sense_intronic"; transcript_name "Gm19938-201"; exon_number 2; exon_id "ENSMUSE00001339227.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTMUSG00000049924.1"; havana_transcript "OTTMUST00000127092.1";
59
+ chr1 HAVANA gene 3680155 3681788 . + . gene_id "ENSMUSG00000102348.1"; gene_type "TEC"; gene_name "Gm10568"; level 2; havana_gene "OTTMUSG00000049922.1";
60
+ chr1 HAVANA transcript 3680155 3681788 . + . gene_id "ENSMUSG00000102348.1"; transcript_id "ENSMUST00000193244.1"; gene_type "TEC"; gene_name "Gm10568"; transcript_type "TEC"; transcript_name "Gm10568-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049922.1"; havana_transcript "OTTMUST00000127090.1";
61
+ chr1 HAVANA exon 3680155 3681788 . + . gene_id "ENSMUSG00000102348.1"; transcript_id "ENSMUST00000193244.1"; gene_type "TEC"; gene_name "Gm10568"; transcript_type "TEC"; transcript_name "Gm10568-201"; exon_number 1; exon_id "ENSMUSE00001341983.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049922.1"; havana_transcript "OTTMUST00000127090.1";
62
+ chr1 HAVANA gene 3752010 3754360 . + . gene_id "ENSMUSG00000102592.1"; gene_type "TEC"; gene_name "Gm38385"; level 2; havana_gene "OTTMUSG00000049923.1";
63
+ chr1 HAVANA transcript 3752010 3754360 . + . gene_id "ENSMUSG00000102592.1"; transcript_id "ENSMUST00000194454.1"; gene_type "TEC"; gene_name "Gm38385"; transcript_type "TEC"; transcript_name "Gm38385-201"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049923.1"; havana_transcript "OTTMUST00000127091.1";
64
+ chr1 HAVANA exon 3752010 3754360 . + . gene_id "ENSMUSG00000102592.1"; transcript_id "ENSMUST00000194454.1"; gene_type "TEC"; gene_name "Gm38385"; transcript_type "TEC"; transcript_name "Gm38385-201"; exon_number 1; exon_id "ENSMUSE00001342074.1"; level 2; transcript_support_level "NA"; tag "basic"; havana_gene "OTTMUSG00000049923.1"; havana_transcript "OTTMUST00000127091.1";
65
+ chr1 ENSEMBL gene 3783876 3783933 . - . gene_id "ENSMUSG00000088333.2"; gene_type "snRNA"; gene_name "Gm27396"; level 3;
66
+ chr1 ENSEMBL transcript 3783876 3783933 . - . gene_id "ENSMUSG00000088333.2"; transcript_id "ENSMUST00000157708.2"; gene_type "snRNA"; gene_name "Gm27396"; transcript_type "snRNA"; transcript_name "Gm27396-201"; level 3; transcript_support_level "NA"; tag "basic";
67
+ chr1 ENSEMBL exon 3783876 3783933 . - . gene_id "ENSMUSG00000088333.2"; transcript_id "ENSMUST00000157708.2"; gene_type "snRNA"; gene_name "Gm27396"; transcript_type "snRNA"; transcript_name "Gm27396-201"; exon_number 1; exon_id "ENSMUSE00000846843.2"; level 3; transcript_support_level "NA"; tag "basic";
68
+ chr1 HAVANA gene 3905739 3986215 . - . gene_id "ENSMUSG00000102343.1"; gene_type "lincRNA"; gene_name "Gm37381"; level 2; havana_gene "OTTMUSG00000049934.1";
69
+ chr1 HAVANA transcript 3905739 3986215 . - . gene_id "ENSMUSG00000102343.1"; transcript_id "ENSMUST00000194643.1"; gene_type "lincRNA"; gene_name "Gm37381"; transcript_type "lincRNA"; transcript_name "Gm37381-202"; level 2; transcript_support_level "3"; tag "basic"; havana_gene "OTTMUSG00000049934.1"; havana_transcript "OTTMUST00000127107.1";
70
+ chr1 HAVANA exon 3986147 3986215 . - . gene_id "ENSMUSG00000102343.1"; transcript_id "ENSMUST00000194643.1"; gene_type "lincRNA"; gene_name "Gm37381"; transcript_type "lincRNA"; transcript_name "Gm37381-202"; exon_number 1; exon_id "ENSMUSE00001344134.1"; level 2; transcript_support_level "3"; tag "basic"; havana_gene "OTTMUSG00000049934.1"; havana_transcript "OTTMUST00000127107.1";
71
+ chr1 HAVANA exon 3985160 3985351 . - . gene_id "ENSMUSG00000102343.1"; transcript_id "ENSMUST00000194643.1"; gene_type "lincRNA"; gene_name "Gm37381"; transcript_type "lincRNA"; transcript_name "Gm37381-202"; exon_number 2; exon_id "ENSMUSE00001337703.1"; level 2; transcript_support_level "3"; tag "basic"; havana_gene "OTTMUSG00000049934.1"; havana_transcript "OTTMUST00000127107.1";
72
+ chr1 HAVANA exon 3905739 3906134 . - . gene_id "ENSMUSG00000102343.1"; transcript_id "ENSMUST00000194643.1"; gene_type "lincRNA"; gene_name "Gm37381"; transcript_type "lincRNA"; transcript_name "Gm37381-202"; exon_number 3; exon_id "ENSMUSE00001345637.1"; level 2; transcript_support_level "3"; tag "basic"; havana_gene "OTTMUSG00000049934.1"; havana_transcript "OTTMUST00000127107.1";
73
+ chr1 HAVANA transcript 3984225 3985984 . - . gene_id "ENSMUSG00000102343.1"; transcript_id "ENSMUST00000192427.1"; gene_type "lincRNA"; gene_name "Gm37381"; transcript_type "lincRNA"; transcript_name "Gm37381-201"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTMUSG00000049934.1"; havana_transcript "OTTMUST00000127108.1";
74
+ chr1 HAVANA exon 3985160 3985984 . - . gene_id "ENSMUSG00000102343.1"; transcript_id "ENSMUST00000192427.1"; gene_type "lincRNA"; gene_name "Gm37381"; transcript_type "lincRNA"; transcript_name "Gm37381-201"; exon_number 1; exon_id "ENSMUSE00001340315.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTMUSG00000049934.1"; havana_transcript "OTTMUST00000127108.1";
75
+ chr1 HAVANA exon 3984225 3984298 . - . gene_id "ENSMUSG00000102343.1"; transcript_id "ENSMUST00000192427.1"; gene_type "lincRNA"; gene_name "Gm37381"; transcript_type "lincRNA"; transcript_name "Gm37381-201"; exon_number 2; exon_id "ENSMUSE00001340468.1"; level 2; transcript_support_level "1"; tag "basic"; havana_gene "OTTMUSG00000049934.1"; havana_transcript "OTTMUST00000127108.1";
76
+ chr1 HAVANA gene 3999557 4409241 . - . gene_id "ENSMUSG00000025900.12"; gene_type "protein_coding"; gene_name "Rp1"; level 2; tag "overlapping_locus"; havana_gene "OTTMUSG00000049985.3";
77
+ chr1 HAVANA transcript 3999557 4409241 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
78
+ chr1 HAVANA exon 4409170 4409241 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 1; exon_id "ENSMUSE00001378580.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
79
+ chr1 HAVANA CDS 4409170 4409187 . - 0 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 1; exon_id "ENSMUSE00001378580.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
80
+ chr1 HAVANA start_codon 4409185 4409187 . - 0 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 1; exon_id "ENSMUSE00001378580.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
81
+ chr1 HAVANA exon 4352202 4352837 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 2; exon_id "ENSMUSE00001403780.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
82
+ chr1 HAVANA CDS 4352202 4352837 . - 0 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 2; exon_id "ENSMUSE00001403780.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
83
+ chr1 HAVANA exon 4351910 4352081 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 3; exon_id "ENSMUSE00001396015.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
84
+ chr1 HAVANA CDS 4351910 4352081 . - 0 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 3; exon_id "ENSMUSE00001396015.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
85
+ chr1 HAVANA exon 4311270 4311433 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 4; exon_id "ENSMUSE00001380053.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
86
+ chr1 HAVANA CDS 4311270 4311433 . - 2 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 4; exon_id "ENSMUSE00001380053.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
87
+ chr1 HAVANA exon 4292926 4293012 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 5; exon_id "ENSMUSE00001377871.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
88
+ chr1 HAVANA CDS 4292926 4293012 . - 0 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 5; exon_id "ENSMUSE00001377871.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
89
+ chr1 HAVANA exon 4284766 4284898 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 6; exon_id "ENSMUSE00001379434.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
90
+ chr1 HAVANA CDS 4284766 4284898 . - 0 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 6; exon_id "ENSMUSE00001379434.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
91
+ chr1 HAVANA exon 4267469 4267620 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 7; exon_id "ENSMUSE00001379919.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
92
+ chr1 HAVANA CDS 4267469 4267620 . - 2 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 7; exon_id "ENSMUSE00001379919.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
93
+ chr1 HAVANA exon 4261527 4261605 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 8; exon_id "ENSMUSE00001380048.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
94
+ chr1 HAVANA CDS 4261527 4261605 . - 0 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 8; exon_id "ENSMUSE00001380048.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
95
+ chr1 HAVANA exon 4245031 4245106 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 9; exon_id "ENSMUSE00001382043.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
96
+ chr1 HAVANA CDS 4245031 4245106 . - 2 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 9; exon_id "ENSMUSE00001382043.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
97
+ chr1 HAVANA exon 4243543 4243619 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 10; exon_id "ENSMUSE00001379965.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
98
+ chr1 HAVANA CDS 4243543 4243619 . - 1 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 10; exon_id "ENSMUSE00001379965.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
99
+ chr1 HAVANA exon 4243417 4243448 . - . gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 11; exon_id "ENSMUSE00001379150.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
100
+ chr1 HAVANA CDS 4243417 4243448 . - 2 gene_id "ENSMUSG00000025900.12"; transcript_id "ENSMUST00000208660.1"; gene_type "protein_coding"; gene_name "Rp1"; transcript_type "protein_coding"; transcript_name "Rp1-203"; exon_number 11; exon_id "ENSMUSE00001379150.1"; level 2; protein_id "ENSMUSP00000146439.1"; transcript_support_level "5"; tag "RNA_Seq_supported_only"; tag "basic"; tag "appris_principal_1"; havana_gene "OTTMUSG00000049985.3"; havana_transcript "OTTMUST00000145515.1";
scte_quant-1.3.3/Data/TE.bed ADDED
@@ -0,0 +1,102 @@
1
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2
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39
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43
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44
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45
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46
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47
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48
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49
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50
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51
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52
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53
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54
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55
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56
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57
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58
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59
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60
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61
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62
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63
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64
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65
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66
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67
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68
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69
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70
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71
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72
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73
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74
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75
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76
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77
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78
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79
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80
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81
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82
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83
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84
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85
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86
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87
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88
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89
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90
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91
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92
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93
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94
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95
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96
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97
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98
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99
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100
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101
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102
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scte_quant-1.3.3/Data/test.bam ADDED
Binary file
scte_quant-1.3.3/LICENSE ADDED
@@ -0,0 +1,21 @@
1
+ MIT License
2
+
3
+ Copyright (c) 2019 Jiangping He, Andrew P. Hutchins & Jiekai Chen
4
+
5
+ Permission is hereby granted, free of charge, to any person obtaining a copy
6
+ of this software and associated documentation files (the "Software"), to deal
7
+ in the Software without restriction, including without limitation the rights
8
+ to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
9
+ copies of the Software, and to permit persons to whom the Software is
10
+ furnished to do so, subject to the following conditions:
11
+
12
+ The above copyright notice and this permission notice shall be included in all
13
+ copies or substantial portions of the Software.
14
+
15
+ THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
16
+ IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
17
+ FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
18
+ AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
19
+ LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
20
+ OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN THE
21
+ SOFTWARE.