Thanks Brad for the reply, but the format conversion sounds bad when deal with multiple samples, especially Paired-End or Mate-Pair samples. It doubles the task. Hence, I'd be more interested to provide csfasta/qual files with -f and -Q1, -Q2 options, as given in Bowtie manual (shown below)
"bowtie also handles input in the form of parallel .csfasta and _QV.qual files. Use -fhttp://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-f to specify the .csfasta files and -Qhttp://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-Q (for unpaired reads) or --Q1http://bowtie-bio..sourceforge.net/manual.shtml#bowtie-options-Q1/--Q2http://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-Q2 (for paired-end reads) to specify the corresponding _QV.qual files. It is not necessary to first convert to FASTQ, though bowtie also handles FASTQ-formatted colorspace reads (with -qhttp://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-q, the default)"
Why should the system spend time in converting the files when the tool itself provide the capability of accepting the original formats.
Pl share your thoughts.
Raj
From: Langhorst, Brad [mailto:Langhorst@neb.com] Sent: Saturday, September 15, 2012 5:46 PM To: Praveen Raj Somarajan Cc: galaxy-dev@lists.bx.psu.edu Subject: Re: [galaxy-dev] Why doesn't bowtie in galaxy accepting colorspacereads directly?
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 Sep 15, 2012, at 6:22 AM, Praveen Raj Somarajan <Praveen.s@ocimumbio.commailto:Praveen.s@ocimumbio.com> 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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