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,


Hsiao lab, BC Public Health Microbiology & Reference Laboratory, BC Centre for 
Disease Control
655 West 12th Avenue, Vancouver, British Columbia, V5Z 4R4 Canada
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