From 113ec5444cacd8fe79f2d4c3a22a1239fc3e39f0 Mon Sep 17 00:00:00 2001 From: DLBPointon Date: Thu, 14 Sep 2023 16:39:02 +0100 Subject: [PATCH] small update --- docs/pacbio.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/docs/pacbio.md b/docs/pacbio.md index 9d582424..9d3cabb3 100644 --- a/docs/pacbio.md +++ b/docs/pacbio.md @@ -2,7 +2,9 @@ Before running the pipeline data has to be in the `fasta.gz` format. Because of the software we use this data with it must also be Long read data as well as single stranded. This means you could use ONT ( excluding duplex reads ) here. -The below commands should help you convert from the format you have to fasta.gz. +The below commands should help you convert from mapped bam to fasta.gz, or from fastq to fasta. + +If your data isn't already in these formats, then let us know and we'll see how we can help. ### BAM -> FASTQ @@ -46,3 +48,9 @@ for i in .fasta; do gzip $i done ``` + +### Or if you're a command line ninja + +```bash +samtools bam2fq {prefix}.bam| seqtk seq -a - | gzip - > {prefix}.fasta.gz +```