Hello William,

The tools in "NGS: QC and manipulation", especially those in the sub-section "AB-SOLiD data" can do the manipulations needed before mapping. It may be helpful to view the screencast at http://usegalaxy.org, center pane, quickie #9.


Hopefully this helps to get you started,

Best,

Jen
Galaxy team


On 7/28/11 2:29 PM, William Light wrote:
I am trying to use bowtie to assign reads to the s. Cerevisiae genome.
  I have data from paired end SOLiD sequencing with two unique six base
pair barcodes.  Can I use bowtie to make csfasta and qual files from my
mixed original data split by bar code?  I know I can use the trim option
to remove the barcode, but how do I specify one only?


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