A researcher here was trying to use Galaxy Picard sam2fastq tool to generate a
single fastq file from a sam file that has a mix of paired and unpaired data.
She was thinking the second input on the sheet might control this:
> Do you want to output a fastq file per read group (two fastq files per read
> group if the group is paired)
> OUTPUT_PER_RG; default=False
But preliminary testing indicates there is no output scenario that includes
both paired and unpaired data in the output (esp. as just one file). I just
wanted to verify that this was the case, since the docs don't talk about this
scenario? We're planning instead to write a little Galaxy tool that does what
she gets accomplished on the command line:
> samtools view -bS in.sam > out.bam
> bamtools convert -format fastq -in in.bam > out.fastq
which includes unpaired reads too.
Thanks for feedback,
Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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