Hi Mayank,

The best option I know of is to do the following:

1 - obtain the sequence identifiers for the unmapped reads by filter the SAM file, then cutting them out
2 - convert the original FASTQ file to FASTA - you should get two output, one for the sequences and one for the quality score values
3 - use the tool "Fetch Sequences -> Extract Genomic DNA". The query is the list from #1, the target is the "genome" from #2. Do this twice - once for seqs, once for quals. This means using the target datasets from #2 as Custom Reference genomes - help about how to do this is here:
http://wiki.galaxyproject.org/Support#Custom_reference_genome
4 - combine the FASTA seq and qual files back to FASTQ

If you will be doing this again, then capture the process into a workflow for future use, in a way creating your own "tool".

Hopefully this helps!

Jen
Galaxy

On 7/18/13 9:40 AM, Mayank Tandon wrote:

I was hoping this question had been asked, but I haven't been able to find it. I want to output the unmapped reads from bowtie as a fastq file for subsequent mapping to other genomes (i.e. the "--un <filename>" option). I know I can extract the unmapped reads by filtering on the bitwise values in the sam output and converting to fastq with the Picard tool, but I'm using colorspace data and bowtie converts them to letterspace. My understanding (coming mostly from forums and personal discussions) was that the color-to-letter conversion was somehow lossy so mapping the colorspace data directly is always preferable.

So the question is: Is bowtie's '--un' option implemented in Galaxy and if so, how do I access it?

Thanks in advance!

Mayank Tandon
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