Hi,
I am trying to map WGS sample data to a set of reference genomes (bacterial) using Bowtie2. I have read the manual and have included the --rg-id option but if I am understanding it correctly, this requires that you specify a specific sample ID. I have hundreds of samples and cannot imagine that this is the only way to include that information in the alignment file.
This is what I am doing:
bowtie2 -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -q --rg-id <text?> -x ref.Index -1 reads_1.fastq -2 reads_2.fastq -S reads_mapped.sam
Whatever is written after --rg-id is included verbatim after @RG and RG:Z: Is there some way to reference the correct position in the fastq file in the command above to include the specific sample ids?
Thank you!
I am trying to map WGS sample data to a set of reference genomes (bacterial) using Bowtie2. I have read the manual and have included the --rg-id option but if I am understanding it correctly, this requires that you specify a specific sample ID. I have hundreds of samples and cannot imagine that this is the only way to include that information in the alignment file.
This is what I am doing:
bowtie2 -D 20 -R 3 -N 0 -L 20 -i S,1,0.50 -q --rg-id <text?> -x ref.Index -1 reads_1.fastq -2 reads_2.fastq -S reads_mapped.sam
Whatever is written after --rg-id is included verbatim after @RG and RG:Z: Is there some way to reference the correct position in the fastq file in the command above to include the specific sample ids?
Thank you!
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