Question: Solid To Fastq For Bowtie
gravatar for Shalabh Sharma
7.3 years ago by
Shalabh Sharma20 wrote:
Hi, I am trying to implement a SOLID pipeline for my solid data. I really like the pipeline used in Galaxy, I was looking for conversion of SOLID to fastq, but it didn't say that how it is achieved in Galaxy. I know for bwa you can use but for bowtie i did not find any program or information. I would really appreciate if you can help me with this, like how it is achieved and where i can download the program used by Galaxy. Thanks Shalabh Sharma Shalabh Sharma Scientific Computing Professional Associate (Bioinformatics Specialist) Department of Marine Sciences University of Georgia Athens, GA 30602-3636
bwa alignment bowtie • 1.6k views
ADD COMMENTlink modified 7.3 years ago by Jennifer Hillman Jackson25k • written 7.3 years ago by Shalabh Sharma20
gravatar for Jennifer Hillman Jackson
7.3 years ago by
United States
Jennifer Hillman Jackson25k wrote:
Hello Shalabh, Galaxy is open source and available here: Check under tools to find: tools/fastq/ Other SOLiD specific tools are under: tools/solid_tools/ The rest is organized in this same general way. This wiki may be helpful: Hopefully this helps. Next time, you can just send to one list, and for development questions, the best list would be Best, Jen Galaxy team -- Jennifer Jackson
ADD COMMENTlink written 7.3 years ago by Jennifer Hillman Jackson25k
Shalabh: To add to Jen's reply bowtie supports SOLiD csfasta and QUAL files natively. However, Galaxy has a tool for converting SOLiD output to fastq here: Tx, anton galaxy team Anton Nekrutenko
ADD REPLYlink written 7.3 years ago by Anton Nekrutenko1.7k
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