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 -f<http://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-f> to 
specify the .csfasta files and 
-Q<http://bowtie-bio.sourceforge.net/manual.shtml#bowtie-options-Q> (for 
unpaired reads) or 
--Q1<http://bowtie-bio..sourceforge.net/manual.shtml#bowtie-options-Q1>/--Q2<http://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 
-q<http://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:langho...@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 
<pravee...@ocimumbio.com<mailto:pravee...@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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