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Question: Solid To Fastq For Bowtie
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gravatar for Shalabh Sharma
7.3 years ago by
Shalabh Sharma • 20
Shalabh Sharma • 20 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 solid2fasta.pl 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
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modified 7.3 years ago by Jennifer Hillman Jackson ♦ 25k • written 7.3 years ago by Shalabh Sharma • 20
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gravatar for Jennifer Hillman Jackson
7.3 years ago by
Jennifer Hillman Jackson ♦ 25k
United States
Jennifer Hillman Jackson ♦ 25k wrote:
Hello Shalabh, Galaxy is open source and available here: http://bitbucket.org/galaxy/galaxy-central/src/ Check under tools to find: tools/fastq/fastq_groomer.py/.xml Other SOLiD specific tools are under: tools/solid_tools/ The rest is organized in this same general way. This wiki may be helpful: http://galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax Hopefully this helps. Next time, you can just send to one list, and for development questions, the best list would be galaxy-dev@bx.psu.edu. http://galaxyproject.org/Support Best, Jen Galaxy team -- Jennifer Jackson http://usegalaxy.org http://galaxyproject.org/Support
ADD COMMENT • link written 7.3 years ago by Jennifer Hillman Jackson ♦ 25k
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: http://bit.ly/pXw3Ic Tx, anton galaxy team Anton Nekrutenko http://nekrut.bx.psu.edu http://usegalaxy.org
ADD REPLY • link written 7.3 years ago by Anton Nekrutenko ♦ 1.7k
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