From 72299894c932bde17ec15f76dd738d333c398b75 Mon Sep 17 00:00:00 2001 From: Chang Ye Date: Sat, 30 Nov 2024 16:46:36 -0600 Subject: [PATCH] docs: update adapter documentation with improved colors and navigation --- docs/adapters.md | 152 +++++++++++++++++++++++------------------------ 1 file changed, 76 insertions(+), 76 deletions(-) diff --git a/docs/adapters.md b/docs/adapters.md index c1a1cf7..661756c 100644 --- a/docs/adapters.md +++ b/docs/adapters.md @@ -4,24 +4,24 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ## Components -- **p5**: 5' Illumina sequencing adapter (shown in light green) -- **p7**: 3' Illumina sequencing adapter (shown in pale green) -- **inline5**: Fixed DNA barcode sequences in brackets () (shown in light blue) -- **inline3**: Fixed DNA barcode sequences in brackets () (shown in light blue) -- **umi5**: 5' Random UMI sequences marked as N (shown in royal blue) -- **umi3**: 3' Random UMI sequences marked as N (shown in cornflower blue) -- **mask5**: Sequences to be masked marked as X (shown in light gray) +- **p5**: 5' Illumina sequencing adapter (shown in light green) +- **p7**: 3' Illumina sequencing adapter (shown in pale green) +- **inline5**: Fixed DNA barcode sequences in brackets () (shown in light cyan) +- **inline3**: Fixed DNA barcode sequences in brackets () (shown in light sky blue) +- **umi5**: 5' Random UMI sequences marked as N (shown in dodger blue) +- **umi3**: 3' Random UMI sequences marked as N (shown in steel blue) +- **mask5**: Sequences to be masked marked as X (shown in gainsboro) - **mask3**: Sequences to be masked marked as X (shown in light gray) -- **strand**: Direction indicator (shown with >, <, or -) +- **strand**: Direction indicator (shown with >, <, or -) ## Built-in Schemes ### DSLIGATION (dsDNA Ligation)
- AGTTCTACAGTCCGACGATCT - > - AGATCGGAAGAGCACACGTC + AGTTCTACAGTCCGACGATCT + > + AGATCGGAAGAGCACACGTC
@@ -32,9 +32,9 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### SMALLRNA (Small RNA Libraries)
- CACGACGCTCTTCCGATCT - > - AGATCGGAAGAGCACACGTC + CACGACGCTCTTCCGATCT + > + AGATCGGAAGAGCACACGTC
@@ -46,12 +46,12 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### INLINE (Custom Barcoded Libraries)
- AGTTCTACAGTCCGACGATC - NNNNN - > - NNNNN + AGTTCTACAGTCCGACGATC + NNNNN + > + NNNNN (ATCACG) - AGATCGGAAGAGCACACGTC + AGATCGGAAGAGCACACGTC
@@ -63,11 +63,11 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### TAKARAV2 (SMARTer® Stranded Protocol V2)
- ACACGACGCTCTTCCGATCT - XXX - < - XXX - AGATCGGAAGAGCACACGTC + ACACGACGCTCTTCCGATCT + XXX + < + XXX + AGATCGGAAGAGCACACGTC
@@ -79,11 +79,11 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### STRANDED (Generic Stranded RNA-seq)
- ACACGACGCTCTTCCGATCT - X - < - XXX - AGATCGGAAGAGCACACGTC + ACACGACGCTCTTCCGATCT + X + < + XXX + AGATCGGAAGAGCACACGTC
@@ -95,12 +95,12 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### TAKARAV3 (SMARTer® Stranded Total RNA-Seq Kit v3)
- ACACGACGCTCTTCCGATCT - XXX - < - XXXXXX - NNNNNNNN - AGATCGGAAGAGCACACGTC + ACACGACGCTCTTCCGATCT + XXX + < + XXXXXX + NNNNNNNN + AGATCGGAAGAGCACACGTC
@@ -112,12 +112,12 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### ECLIP6 (eCLIP Protocol)
- ACACGACGCTCTTCCGATCT - XX - < - X + ACACGACGCTCTTCCGATCT + XX + < + X NNNNNN - AGATCGGAAGAGCACACGTC + AGATCGGAAGAGCACACGTC
@@ -129,12 +129,12 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### ECLIP10 (Extended eCLIP Protocol)
- ACACGACGCTCTTCCGATCT - XX - < - X + ACACGACGCTCTTCCGATCT + XX + < + X NNNNNNNNNN - AGATCGGAAGAGCACACGTC + AGATCGGAAGAGCACACGTC
@@ -146,13 +146,13 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### SACSEQV3 (SAC-seq Protocol V3)
- AGTTCTACAGTCCGACGATCT + AGTTCTACAGTCCGACGATCT NNNNNNNN - X - > - XX + X + > + XX NNNNNNNN - AGATCGGAAGAGCACACGTC + AGATCGGAAGAGCACACGTC
@@ -164,11 +164,11 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### XGENRNA (xGen RNA Library Prep)
- ACACGACGCTCTTCCGATCT - XXXXXX - < - XXXXXXXXXXXXXXX - AGATCGGAAGAGCACACGTC + ACACGACGCTCTTCCGATCT + XXXXXX + < + XXXXXXXXXXXXXXX + AGATCGGAAGAGCACACGTC
@@ -180,11 +180,11 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### XGENMETHY (xGen Methyl-Seq)
- ACACGACGCTCTTCCGATCT - XX - > - XXXXXXXXXX - AGATCGGAAGAGCACACGTC + ACACGACGCTCTTCCGATCT + XX + > + XXXXXXXXXX + AGATCGGAAGAGCACACGTC
@@ -196,11 +196,11 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### XGENSNMC (snmC-seq Protocol)
- ACACGACGCTCTTCCGATCT - XXXXXX - > - XXXXXXXXXXXXXXX - AGATCGGAAGAGCACACGTC + ACACGACGCTCTTCCGATCT + XXXXXX + > + XXXXXXXXXXXXXXX + AGATCGGAAGAGCACACGTC
@@ -212,11 +212,11 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### PBAT (Post-Bisulfite Adapter Tagging)
- ACACGACGCTCTTCCGATCT - XXXXXX - < - XXXXXX - AGATCGGAAGAGCACACGTC + ACACGACGCTCTTCCGATCT + XXXXXX + < + XXXXXX + AGATCGGAAGAGCACACGTC
@@ -228,9 +228,9 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### NEXTERA (ATAC-seq)
- AGATGTGTATAAGAGACAG - > - CTGTCTCTTATACACATCT + AGATGTGTATAAGAGACAG + > + CTGTCTCTTATACACATCT
@@ -242,9 +242,9 @@ CutSeq supports various built-in adapter schemes for different NGS library prepa ### ILLUMINARNA (Illumina Stranded RNA-Seq)
- AGATGTGTATAAGAGACAG - < - CTGTCTCTTATACACATCT + AGATGTGTATAAGAGACAG + < + CTGTCTCTTATACACATCT