Re: [galaxy-user] Why doesn't bowtie in galaxy accepting colorspace reads directly?

[Jennifer Jackson]

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 +
From:   Langhorst, Brad 
To: Praveen Raj Somarajan 
CC: 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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[galaxy-user] Why doesn't bowtie in galaxy accepting colorspace reads directly?

[Praveen Raj Somarajan]

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.


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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.

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