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?
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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I have created fixed-step wiggle files for a project that I am working on, but I am wondering if there is an easy way to transform the values by a correction factor to account for differences in in the number of reads for two different samples (one had 1.5 million or so, the other had 6.6million).
galaxy-user@lists.galaxyproject.org
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Jennifer Jackson -
William Light