Re: [galaxy-user] user reference vs. built-in index

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Re: [galaxy-user] user reference vs. built-in index

Viren Patel
Hi Kelly. I just wanted to follow-up on this issue. I did some more
tests and it seems that the problem may be because the
fragement headers in my custom reference multi-fasta contain the
coordinates of the fragment in the form chr:start-stop. Upon mapping
with bowtie, the resultant SAM file contains the headers (as expected).
But the BAM-to-pileup tool does not play well with such headers. It
seems the BAM-to-pileup tool expects headers in only chr format. Since
there does not appear to be a tool on galaxy to convert chr:start-stop
to chr format in a SAM file (note: this also requires modification of
the next column in the SAM file), the solution at this point is to
download the SAM file, locally apply the fix, re-upload the SAM file and
run the BAM-to-pileup tool with a built-in index (mm9 in my case). Even
at this step, I still can't use my custom reference for the pileup
because it contains headers in chr:start-stop format. Thoughts?

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