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 <Langhorst@neb.com> 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 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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