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broadinstitute / CODECsuite

analysis pipeline for CODEC data
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Trimmed BAM name #5

Closed wclee47 closed 1 year ago

wclee47 commented 1 year ago

Hi, when running codec trim, it seems that "-s" parameter doesn't work. When I followed the instructions here:

codec trim -1 demux_outprefix.sample_A.1.fastq.gz -2 demux_outprefix.sample_A.2.fastq.gz -o trim_outprefix -u 3 -U 3 -f 2 -t 2 -s sample_A

It produces the trimmed BAM named "trim_outprefix.trim.bam", and doesn't include "sample_A" in the name.

Could you please check the code.

Thanks!

Won-Chul

ruolin commented 1 year ago

Hi @wclee47 thank you for your question. The -o is supposed to be the output file prefix whereas -s is the read_group name in the bam header. I think my example command line is confusing. It may be easier to understand if -o and -s are the same.

wclee47 commented 1 year ago

Hi ruolin, thanks for the explanation.

Yes, your example was a bit confusing because the output prefix is set to be "trim_outprefix" and the resulting bam file has "trim_outprefix.sample_A". Hope it to be more clarified.

Anyway thank you very much for the help!

Won-Chul