Repost for galaxy-user readers.

Raj, please try not to double post to both lists going forward.

Thanks,

Jen
Galaxy team


-------- Original Message --------
Subject:        Re: [galaxy-dev] Why doesn't bowtie in galaxy accepting
colorspace reads directly?
Date:   Sat, 15 Sep 2012 12:16:09 +0000
From:   Langhorst, Brad <langho...@neb.com>
To:     Praveen Raj Somarajan <pravee...@ocimumbio.com>
CC:     galaxy-...@lists.bx.psu.edu <galaxy-...@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

On 9/15/12 3:22 AM, Praveen Raj Somarajan wrote:
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


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