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) > YesNo > 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, d. Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for Disease Control 655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada ___________________________________________________________ Please keep all replies on the list by using "reply all" in your mail client. To manage your subscriptions to this and other Galaxy lists, please use the interface at: https://lists.galaxyproject.org/ To search Galaxy mailing lists use the unified search at: http://galaxyproject.org/search/mailinglists/
