Why Doesn'T Bowtie In Galaxy Accepting Colorspace Reads Directly?

Question: Why Doesn'T Bowtie In Galaxy Accepting Colorspace Reads Directly?

6.2 years ago by

Hi All, I'm wondering why the Bowtie version in (even latest) Galaxy does NOT support .csfasta/.qual input files directly, though it is mentioned under "Map with Bowtie for SOLiD". This is the case of "BWA for SOLiD" as well. One would expect direct support on colorspace files. Do you have any plans of implementing this?I see this would be a great support to SOLiD users. Look forward to your comments Thanks, Raj ________________________________ This e-mail contains PRIVILEGED AND CONFIDENTIAL INFORMATION intended solely for the use of the addressee(s). If you are not the intended recipient, please notify the sender by e-mail and delete the original message. Further, you are not to copy, disclose, or distribute this e-mail or its contents to any other person and any such actions that are unlawful. This e-mail may contain viruses. Ocimum Biosolutions has taken every reasonable precaution to minimize this risk, but is not liable for any damage you may sustain as a result of any virus in this e-mail. You should carry out your own virus checks before opening the e-mail or attachment. The information contained in this email and any attachments is confidential and may be subject to copyright or other intellectual property protection. If you are not the intended recipient, you are not authorized to use or disclose this information, and we request that you notify us by reply mail or telephone and delete the original message from your mail system. OCIMUMBIO SOLUTIONS (P) LTD

bwa alignment bowtie • 1.1k views

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modified 6.1 years ago by Jennifer Hillman Jackson ♦ 25k • written 6.2 years ago by Praveen Raj Somarajan • 100

6.1 years ago by

Jennifer Hillman Jackson ♦ 25k

United States

Jennifer Hillman Jackson ♦ 25k wrote:

Repost for galaxy-user readers. Raj, please try not to double post to both lists going forward. Thanks, Jen Galaxy team Subject: Re: [galaxy-dev] Why doesn't bowtie in galaxy accepting colorspace reads directly? Date: Sat, 15 Sep 2012 12:16:09 +0000 To: Praveen Raj Somarajan <praveen.s@ocimumbio.com> CC: galaxy-dev@lists.bx.psu.edu <galaxy-dev@lists.bx.psu.edu> Raj: It does support colorspace files, but you have to convert them to fastq first. That sounds bad, but you don't have to convert to basespace to store the data in fastq, so there is no loss of data - just one extra step. https://main.g2.bx.psu.edu/tool_runner?tool_id=fastq_combiner Only bowtie 1.x supports colorspace (and that's all that's available on the public galaxy anyway) https://main.g2.bx.psu.edu/tool_runner?tool_id=bowtie_color_wrapper Brad -- Jennifer Jackson http://galaxyproject.org

ADD COMMENT • link written 6.1 years ago by Jennifer Hillman Jackson ♦ 25k

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