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
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:


To manage your subscriptions to this and other Galaxy lists,
please use the interface at:


To search Galaxy mailing lists use the unified search at:


Reply via email to