cutseq 0.0.63__tar.gz → 0.0.65__tar.gz
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- {cutseq-0.0.63 → cutseq-0.0.65}/.pre-commit-config.yaml +5 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/PKG-INFO +1 -1
- cutseq-0.0.65/cutseq/adapters.toml +158 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/cutseq/common.py +22 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/cutseq/run.py +21 -3
- cutseq-0.0.65/docs/adapters.md +141 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/pyproject.toml +1 -1
- cutseq-0.0.65/scripts/update_adapter_docs.py +213 -0
- cutseq-0.0.63/cutseq/adapters.toml +0 -191
- cutseq-0.0.63/docs/adapters.md +0 -243
- cutseq-0.0.63/scripts/update_adapter_docs.py +0 -135
- {cutseq-0.0.63 → cutseq-0.0.65}/.github/FUNDING.yml +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/.github/workflows/docs.yaml +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/.github/workflows/python-publish.yml +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/.gitignore +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/README.md +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/docs/CNAME +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/docs/_config.yml +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/docs/explain_library.png +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/docs/favicon.ico +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/docs/index.md +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/docs/takaraV3.png +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/test/input_R1.fq.gz +0 -0
- {cutseq-0.0.63 → cutseq-0.0.65}/test/input_R2.fq.gz +0 -0
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@@ -10,3 +10,8 @@ repos:
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# that are part of the commit or that are modified by the hook.
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# If docs/adapters.md is tracked by git, changes made by the script
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# will be automatically added to the staging area.
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- repo: https://github.com/astral-sh/uv-pre-commit
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# uv version.
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rev: 0.7.6
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hooks:
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- id: uv-lock
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@@ -0,0 +1,158 @@
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# Built-in adapter schemes for cutseq
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# RNA library
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[SMALLRNA]
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scheme = "AGTTCTACAGTCCGACGATC>AGATCGGAAGAGCACACGTC"
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description_name = "Small RNA Libraries"
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points = [
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"Used for small RNA sequencing",
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"Double ligation method",
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"Forward orientation",
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"Optional 2nt trimming on both ends for quality",
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]
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[SMRNA]
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scheme = "AGTTCTACAGTCCGACGATC>TGGAATTCTCGGGTGCCAAG"
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description_name = "Small RNA (Legacy)"
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points = [
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"Legacy version for small RNA sequencing",
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"Refer to library preparation protocol for details.",
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]
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[INLINE]
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scheme = "AGTTCTACAGTCCGACGATCNNNNN>NNNNN(ATCACG)AGATCGGAAGAGCACACGTC"
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description_name = "Custom Barcoded Libraries"
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points = [
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"Used for libraries with inline barcodes",
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"Dual UMI design (5nt each)",
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"Forward orientation",
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"Contains fixed inline barcode (ATCACG)",
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]
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[TAKARAV2]
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scheme = "ACACGACGCTCTTCCGATCTXXX<XXXAGATCGGAAGAGCACACGTC"
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description_name = "Takara V2"
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points = [
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"Contains masked regions (XXX)",
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"Refer to Takara V2 library preparation protocol for details.",
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]
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[STRANDED]
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scheme = "ACACGACGCTCTTCCGATCTX<XXXAGATCGGAAGAGCACACGTC"
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description_name = "Stranded RNA"
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points = [
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"Contains masked regions (X, XXX)",
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"Refer to stranded RNA library preparation protocol for details.",
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]
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[UNSTRANDED]
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scheme = "ACACGACGCTCTTCCGATCTXX-XXAGATCGGAAGAGCACACGTC"
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description_name = "Unstranded RNA/DNA"
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points = [
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"Contains masked regions (XX)",
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"Refer to library preparation protocol for details.",
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]
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[TAKARAV3]
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scheme = "ACACGACGCTCTTCCGATCTXXX<XXXXXXNNNNNNNNAGATCGGAAGAGCACACGTC"
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description_name = "Takara V3"
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points = [
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"Contains masked regions (XXX, XXXXXX)",
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"Contains UMI sequences (NNNNNNNN)",
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"Refer to Takara V3 library preparation protocol for details.",
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]
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[ECLIP6]
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scheme = "ACACGACGCTCTTCCGATCTXX<XNNNNNNAGATCGGAAGAGCACACGTC"
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description_name = "eCLIP (6nt UMI)"
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points = [
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"Contains masked regions (XX, X)",
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"Contains UMI sequences (NNNNNN)",
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"Used for eCLIP experiments with a 6-nucleotide UMI.",
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]
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[ECLIP10]
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scheme = "ACACGACGCTCTTCCGATCTXX<XNNNNNNNNNNAGATCGGAAGAGCACACGTC"
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description_name = "eCLIP (10nt UMI)"
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points = [
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"Contains masked regions (XX, X)",
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"Contains UMI sequences (NNNNNNNNNN)",
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"Used for eCLIP experiments with a 10-nucleotide UMI.",
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]
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[SACSEQ]
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scheme = "ACACGACGCTCTTCCGATCT<XXXXNNNNNNAGATCGGAAGAGCACACGTC"
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description_name = "SAC-Seq"
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points = [
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"Contains masked regions (XXXX)",
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"Contains UMI sequences (NNNNNN)",
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"Used for SAC-Seq (Single-cell RNA-Seq) or similar protocols.",
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]
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[SACSEQV3]
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scheme = "ACACGACGCTCTTCCGATCTNNNNNNNNX>XXNNNNNNNNAGATCGGAAGAGCACACGTC"
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description_name = "SAC-Seq V3"
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points = [
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"Contains masked regions (X, XX)",
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"Contains dual UMI sequences (NNNNNNNN on both sides)",
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"Refer to SAC-Seq V3 library preparation protocol for details.",
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]
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[XGENRNA]
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scheme = "ACACGACGCTCTTCCGATCTXXXXXX<XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC"
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description_name = "xGen RNA"
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points = [
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"Contains extensive masked regions (XXXXXX, XXXXXXXXXXXXXXX)",
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"Likely for specific xGen RNA library preps, check protocol.",
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]
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[ILLUMINARNA]
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scheme = "AGATGTGTATAAGAGACAG<CTGTCTCTTATACACATCT"
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description_name = "Illumina Stranded RNA (Nextera-based)"
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points = ["Uses Nextera-style adapter sequences."]
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# DNA library
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[DSLIGATION]
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scheme = "ACACGACGCTCTTCCGATCT>AGATCGGAAGAGCACACGTC"
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description_name = "dsDNA Ligation"
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points = [
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"Basic dsDNA ligation with A-tailing",
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"No UMIs or special trimming needed",
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]
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# xGenDNA = "ACACGACGCTCTTCCGATCTXXX>(CCCCCCCCCCCCCCCCCCCC;noninternal;e=0.5;o=1)AGATCGGAAGAGCACACGTC" # Commented out
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[XGENMETHY]
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scheme = "ACACGACGCTCTTCCGATCTXX>XXXXXXXXXXAGATCGGAAGAGCACACGTC"
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description_name = "xGen Methyl-Seq"
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points = [
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"Contains masked regions (XX, XXXXXXXXXX)",
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"Designed for xGen Methyl-Seq library kits.",
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]
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[XGENSNMC]
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scheme = "ACACGACGCTCTTCCGATCTXXXXXX>XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC"
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description_name = "xGen snmC-Seq"
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points = [
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"Contains extensive masked regions (XXXXXX, XXXXXXXXXXXXXXX)",
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"Designed for xGen single-nucleus methylC-Seq (snmC-Seq) library kits.",
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]
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[PBAT]
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scheme = "ACACGACGCTCTTCCGATCTXXXXXX<XXXXXXAGATCGGAAGAGCACACGTC"
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description_name = "PBAT (Post-Bisulfite Adapter Tagging)"
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points = [
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"Contains masked regions (XXXXXX on both sides)",
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"Used for PBAT-style bisulfite sequencing libraries.",
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]
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[NEXTERA]
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scheme = "AGATGTGTATAAGAGACAG>CTGTCTCTTATACACATCT"
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description_name = "Nextera (General)"
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points = [
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"Standard Nextera transposase-based library preparation.",
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"No UMIs by default in this basic scheme.",
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"Usually used for ATAC-seq libraries.",
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]
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"mask3": self.mask3.fw,
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"strand": self.strand,
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}
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def print_builtin_adapters():
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"""
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Print all built-in adapter names and their schemes in a well-organized, pretty table.
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"""
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from textwrap import wrap
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print("\nBuilt-in adapter schemes:\n")
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# Find the max width for name and scheme for alignment
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max_name_len = max(len(name) for name in BUILDIN_ADAPTERS)
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max_scheme_len = max(len(scheme) for scheme in BUILDIN_ADAPTERS.values())
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# Header
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print(f"{'Name'.ljust(max_name_len)} {'Scheme'}")
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print(f"{'-'*max_name_len} {'-'*max(30, min(max_scheme_len, 100))}")
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# Print each adapter, wrapping long schemes
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for name, scheme in BUILDIN_ADAPTERS.items():
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wrapped_scheme = wrap(scheme, width=100)
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print(f"{name.ljust(max_name_len)} {wrapped_scheme[0]}")
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for cont in wrapped_scheme[1:]:
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print(f"{' '*max_name_len} {cont}")
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print("\nUse the adapter name with -A/--adapter-name, or the scheme string with -a/--adapter-scheme.\n")
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from cutadapt.utils import Progress
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from .common import
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from .common import load_adapters, BarcodeConfig, remove_fq_suffix, print_builtin_adapters
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# Initialize built-in adapters at the top so it's available for argument parsing
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BUILDIN_ADAPTERS = load_adapters()
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# monkey patching ....
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original_method = Statistics._collect_modifier
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parser.add_argument(
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"input_file",
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type=str,
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nargs="
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nargs="?",
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help="Input file path for NGS data, one or two files (for single or paired-end reads).",
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# output file can be number of files matching the input files, if not provided it will generate based on the output prefix,
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"-V", "--version", action="version", version=f"%(prog)s {__version__}"
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parser.add_argument(
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"--list-adapters",
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action="store_true",
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help="List all built-in adapter names and their schemes, then exit."
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)
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# Check if no arguments were provided
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parser.print_help(sys.stdout)
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args = parser.parse_args()
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if args.list_adapters:
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print_builtin_adapters()
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sys.exit(0)
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# Check if input file is provided
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logging.error("Input file is required.")
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sys.exit(1)
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if args.adapter_name is not None:
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if args.adapter_scheme is not None:
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logging.info("Adapter scheme is provided, ignoring adapter name.")
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args.adapter_scheme = BUILDIN_ADAPTERS.get(args.adapter_name.upper())
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if args.adapter_scheme is None:
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logging.error(
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f"Adapter name '{args.adapter_name}
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f"Adapter name '{args.adapter_name} not found in built-in adapters."
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# sys.exit(1) # Consider exiting if a bad name is given and no scheme
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# Adapter Schemes
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This file is auto-generated by `scripts/update_adapter_docs.py`. Do not edit manually.
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This document lists the built-in adapter schemes available in `cutseq`. These can be used with the `-A` or `--adapter-name` option in the `cutseq run` command.
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### SMALLRNA (Small RNA Libraries)
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<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: AGTTCTACAGTCCGACGATC>AGATCGGAAGAGCACACGTC" data-scheme="AGTTCTACAGTCCGACGATC>AGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGTTCTACAGTCCGACGATC</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
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- Used for small RNA sequencing
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- Double ligation method
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- Forward orientation
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- Optional 2nt trimming on both ends for quality
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|
+
|
|
14
|
+
---
|
|
15
|
+
### SMRNA (Small RNA (Legacy))
|
|
16
|
+
|
|
17
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: AGTTCTACAGTCCGACGATC>TGGAATTCTCGGGTGCCAAG" data-scheme="AGTTCTACAGTCCGACGATC>TGGAATTCTCGGGTGCCAAG"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGTTCTACAGTCCGACGATC</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">TGGAATTCTCGGGTGCCAAG</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
18
|
+
- Legacy version for small RNA sequencing
|
|
19
|
+
- Refer to library preparation protocol for details.
|
|
20
|
+
|
|
21
|
+
---
|
|
22
|
+
### INLINE (Custom Barcoded Libraries)
|
|
23
|
+
|
|
24
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: AGTTCTACAGTCCGACGATCNNNNN>NNNNN(ATCACG)AGATCGGAAGAGCACACGTC" data-scheme="AGTTCTACAGTCCGACGATCNNNNN>NNNNN(ATCACG)AGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGTTCTACAGTCCGACGATC</span><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNN</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNN</span><span style="background-color: #FFD700; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ATCACG</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
25
|
+
- Used for libraries with inline barcodes
|
|
26
|
+
- Dual UMI design (5nt each)
|
|
27
|
+
- Forward orientation
|
|
28
|
+
- Contains fixed inline barcode (ATCACG)
|
|
29
|
+
|
|
30
|
+
---
|
|
31
|
+
### TAKARAV2 (Takara V2)
|
|
32
|
+
|
|
33
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXXX<XXXAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXXX<XXXAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXX</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
34
|
+
- Contains masked regions (XXX)
|
|
35
|
+
- Refer to Takara V2 library preparation protocol for details.
|
|
36
|
+
|
|
37
|
+
---
|
|
38
|
+
### STRANDED (Stranded RNA)
|
|
39
|
+
|
|
40
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTX<XXXAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTX<XXXAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">X</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXX</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
41
|
+
- Contains masked regions (X, XXX)
|
|
42
|
+
- Refer to stranded RNA library preparation protocol for details.
|
|
43
|
+
|
|
44
|
+
---
|
|
45
|
+
### UNSTRANDED (Unstranded RNA/DNA)
|
|
46
|
+
|
|
47
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXX-XXAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXX-XXAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">-</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XX</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
48
|
+
- Contains masked regions (XX)
|
|
49
|
+
- Refer to library preparation protocol for details.
|
|
50
|
+
|
|
51
|
+
---
|
|
52
|
+
### TAKARAV3 (Takara V3)
|
|
53
|
+
|
|
54
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXXX<XXXXXXNNNNNNNNAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXXX<XXXXXXNNNNNNNNAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXX</span><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNNNNN</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
55
|
+
- Contains masked regions (XXX, XXXXXX)
|
|
56
|
+
- Contains UMI sequences (NNNNNNNN)
|
|
57
|
+
- Refer to Takara V3 library preparation protocol for details.
|
|
58
|
+
|
|
59
|
+
---
|
|
60
|
+
### ECLIP6 (eCLIP (6nt UMI))
|
|
61
|
+
|
|
62
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXX<XNNNNNNAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXX<XNNNNNNAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">X</span><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNNN</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
63
|
+
- Contains masked regions (XX, X)
|
|
64
|
+
- Contains UMI sequences (NNNNNN)
|
|
65
|
+
- Used for eCLIP experiments with a 6-nucleotide UMI.
|
|
66
|
+
|
|
67
|
+
---
|
|
68
|
+
### ECLIP10 (eCLIP (10nt UMI))
|
|
69
|
+
|
|
70
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXX<XNNNNNNNNNNAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXX<XNNNNNNNNNNAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">X</span><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNNNNNNN</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
71
|
+
- Contains masked regions (XX, X)
|
|
72
|
+
- Contains UMI sequences (NNNNNNNNNN)
|
|
73
|
+
- Used for eCLIP experiments with a 10-nucleotide UMI.
|
|
74
|
+
|
|
75
|
+
---
|
|
76
|
+
### SACSEQ (SAC-Seq)
|
|
77
|
+
|
|
78
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCT<XXXXNNNNNNAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCT<XXXXNNNNNNAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXX</span><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNNN</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
79
|
+
- Contains masked regions (XXXX)
|
|
80
|
+
- Contains UMI sequences (NNNNNN)
|
|
81
|
+
- Used for SAC-Seq (Single-cell RNA-Seq) or similar protocols.
|
|
82
|
+
|
|
83
|
+
---
|
|
84
|
+
### SACSEQV3 (SAC-Seq V3)
|
|
85
|
+
|
|
86
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTNNNNNNNNX>XXNNNNNNNNAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTNNNNNNNNX>XXNNNNNNNNAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNNNNN</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">X</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XX</span><span style="background-color: #B2EBF2; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">NNNNNNNN</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
87
|
+
- Contains masked regions (X, XX)
|
|
88
|
+
- Contains dual UMI sequences (NNNNNNNN on both sides)
|
|
89
|
+
- Refer to SAC-Seq V3 library preparation protocol for details.
|
|
90
|
+
|
|
91
|
+
---
|
|
92
|
+
### XGENRNA (xGen RNA)
|
|
93
|
+
|
|
94
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXXXXXX<XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXXXXXX<XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXXXXXXXXXXX</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
95
|
+
- Contains extensive masked regions (XXXXXX, XXXXXXXXXXXXXXX)
|
|
96
|
+
- Likely for specific xGen RNA library preps, check protocol.
|
|
97
|
+
|
|
98
|
+
---
|
|
99
|
+
### ILLUMINARNA (Illumina Stranded RNA (Nextera-based))
|
|
100
|
+
|
|
101
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: AGATGTGTATAAGAGACAG<CTGTCTCTTATACACATCT" data-scheme="AGATGTGTATAAGAGACAG<CTGTCTCTTATACACATCT"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATGTGTATAAGAGACAG</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">CTGTCTCTTATACACATCT</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
102
|
+
- Uses Nextera-style adapter sequences.
|
|
103
|
+
|
|
104
|
+
---
|
|
105
|
+
### DSLIGATION (dsDNA Ligation)
|
|
106
|
+
|
|
107
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCT>AGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCT>AGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
108
|
+
- Basic dsDNA ligation with A-tailing
|
|
109
|
+
- No UMIs or special trimming needed
|
|
110
|
+
|
|
111
|
+
---
|
|
112
|
+
### XGENMETHY (xGen Methyl-Seq)
|
|
113
|
+
|
|
114
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXX>XXXXXXXXXXAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXX>XXXXXXXXXXAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXXXXXX</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
115
|
+
- Contains masked regions (XX, XXXXXXXXXX)
|
|
116
|
+
- Designed for xGen Methyl-Seq library kits.
|
|
117
|
+
|
|
118
|
+
---
|
|
119
|
+
### XGENSNMC (xGen snmC-Seq)
|
|
120
|
+
|
|
121
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXXXXXX>XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXXXXXX>XXXXXXXXXXXXXXXAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXXXXXXXXXXX</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
122
|
+
- Contains extensive masked regions (XXXXXX, XXXXXXXXXXXXXXX)
|
|
123
|
+
- Designed for xGen single-nucleus methylC-Seq (snmC-Seq) library kits.
|
|
124
|
+
|
|
125
|
+
---
|
|
126
|
+
### PBAT (PBAT (Post-Bisulfite Adapter Tagging))
|
|
127
|
+
|
|
128
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: ACACGACGCTCTTCCGATCTXXXXXX<XXXXXXAGATCGGAAGAGCACACGTC" data-scheme="ACACGACGCTCTTCCGATCTXXXXXX<XXXXXXAGATCGGAAGAGCACACGTC"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">ACACGACGCTCTTCCGATCT</span><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXX</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;"><</span></div><span style="background-color: #DCDCDC; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">XXXXXX</span><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATCGGAAGAGCACACGTC</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
129
|
+
- Contains masked regions (XXXXXX on both sides)
|
|
130
|
+
- Used for PBAT-style bisulfite sequencing libraries.
|
|
131
|
+
|
|
132
|
+
---
|
|
133
|
+
### NEXTERA (Nextera (General))
|
|
134
|
+
|
|
135
|
+
<div class="adapter-scheme" style="margin-bottom: 15px; position: relative;"><div class="copy-scheme-raw" style="display: flex; flex-wrap: nowrap; align-items: center; font-family: monospace; font-size: 14px; border: 1px solid #ccc; padding: 5px; border-radius: 5px; overflow-x: auto; cursor: pointer; background: #f8f8f8; transition: box-shadow 0.2s;" title="Click to copy scheme: AGATGTGTATAAGAGACAG>CTGTCTCTTATACACATCT" data-scheme="AGATGTGTATAAGAGACAG>CTGTCTCTTATACACATCT"><span style="background-color: #A8E6CF; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">AGATGTGTATAAGAGACAG</span><div style="position: relative; width: 30px; height: 30px; margin: 0 2px; text-align: center; line-height: 30px;"><div style="background-color: #FF6F61; width: 100%; height: 100%; position: absolute; top: 0; left: 0; clip-path: polygon(25% 0%, 75% 0%, 100% 50%, 75% 100%, 25% 100%, 0% 50%);"></div><span style="position: relative; z-index: 1; color: white; font-weight: bold;">></span></div><span style="background-color: #D1E8D1; padding: 5px 8px; margin: 0 2px; border-radius: 3px; white-space: nowrap;">CTGTCTCTTATACACATCT</span></div><div class="scheme-raw-tooltip" style="display:none; position:absolute; top:-30px; left:0; background:#222; color:#fff; padding:3px 8px; border-radius:4px; font-size:12px; z-index:10;">Copied!</div></div>
|
|
136
|
+
- Standard Nextera transposase-based library preparation.
|
|
137
|
+
- No UMIs by default in this basic scheme.
|
|
138
|
+
- Usually used for ATAC-seq libraries.
|
|
139
|
+
|
|
140
|
+
---
|
|
141
|
+
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|