From 233882d2dd58b6e88c9d42a8a9183a2c7711e4f4 Mon Sep 17 00:00:00 2001 From: Armin Toepfer Date: Mon, 18 Dec 2023 13:59:24 +0100 Subject: [PATCH] Improve get-started.md --- docs/get-started.md | 19 ++++++++++++------- 1 file changed, 12 insertions(+), 7 deletions(-) diff --git a/docs/get-started.md b/docs/get-started.md index 4e98c7a..2d7f8e2 100644 --- a/docs/get-started.md +++ b/docs/get-started.md @@ -22,9 +22,13 @@ Reads can be in following formats: | CCS / HiFi | FASTQ [gzipped] | `.fastq[.gz]` | ### Barcodes -Barcodes have to be in FASTA format `.fasta`, one entry per barcode -sequence, **no duplicate** sequences, only upper-case bases, orientation -agnostic (forward or reverse-complement, but **NOT** reversed). Example: +Barcodes have to be in FASTA format `.fasta`: + - one entry per barcode sequence, + - **no duplicate** sequences, + - only upper-case bases, + - orientation agnostic (forward or reverse-complement, but **NOT** reversed). + +Example: >bc1000 CTCTACTTACTTACTG @@ -33,9 +37,10 @@ agnostic (forward or reverse-complement, but **NOT** reversed). Example: >bc1002 AATATACCTATCATTA -Please name your barcodes with an alphabetic character prefix to avoid -later confusion of barcode name and index. Duplicate names or sequences -are not permitted. +Barcode name rules: + - please start with an alphabetic character prefix to avoid later confusion of barcode name and index, + - dashes are not allowed, + - **no duplicate** names. **Can I have upper- and lower-case bases in my barcodes?**\ You can, but lima is case-insensitive and will convert them to upper case before @@ -74,7 +79,7 @@ For CCS / HiFi data, use following compatibility matrix: HiFi run from *BAM* with **symmetric** barcodes: lima .hifi_reads.bam barcodes.fasta .demux.bam --hifi-preset SYMMETRIC - + HiFi run from *FASTQ* with **asymmetric** barcodes: lima .hifi_reads.fq.gz barcodes.fasta .demux.fastq --hifi-preset ASYMMETRIC