Adding multiple RG values in Bowtie2 when aligning with multiple fastq

Question

[Runscar]

Hello,

I'm interested in keeping track of different sequence files as I go through a pipeline of mapping reads and calling variants.

I thought I might be able to add distinct read groups for each sequence file used to produce a bowtie2 alignment using something similar to this:

bowtie2 -q --very-sensitive -x RefGenome --rg-id first,second -rg PL:ILLUMINA,ILLUMINA -rg DS:NovaSeq,NovaSeq -rg PU:HFJ2WCCX2,HC3LCDSX2 -1 Seq1_R1.fq,Seq2_R1.fq  -2 Seq1_R2.fq,Seq2_R2.fq

but checking with samtools view -H Test_RG.bam and samtools stats --split RG Test_RG.bam this just produces a single RG called "first,second" for the two sequence files.

Is there a way to assign a distinct read group per sequence file in a single bam file generated with bowtie2? The bowtie2 manual entry for --rg-id and --rg doesn't explicitly say anything about multiple sequence files.

Many thanks.

Answer 1

[Runscar]

Well, for posterity sake, what I ended up doing was mapping each file separately with its own RGs specified, and then merging the bam files after the fact.