Thanks Brad. I can probably look into the xml tool definition and change.
Meantime, I'll go with the current solution of converting files.
Raj
From: Langhorst, Brad [mailto:langho...@neb.com]
Sent: Monday, September 17, 2012 5:15 PM
To: Praveen Raj Somarajan
Cc: galaxy-dev@lists.bx.psu.edu
Subject: Re: [galaxy-dev] Why doesn't bowtie in galaxy acceptingcolorspacereads
directly?
Raj:
It would not be a big job to add some parameters to the xml tool definition for
bowtie... if you're running this on your own instance.
If you're planning to run on the public galaxy, you'll probably get results
more quickly by doing the conversion than by convincing the managers of that
system to implement a change.
If it's any consolation, it's not a terribly expensive conversion - we do it
for all of our SOLiD data now.
Brad
On Sep 17, 2012, at 4:18 AM, Praveen Raj Somarajan
<pravee...@ocimumbio.com<mailto:pravee...@ocimumbio.com>>
wrote:
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<http://neb.com>]
Sent: Saturday, September 15, 2012 5:46 PM
To: Praveen Raj Somarajan
Cc: galaxy-dev@lists.bx.psu.edu<mailto: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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The information contained in this email and any attachments is confidential and
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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.
OCIMUMBIO SOLUTIONS (P) LTD
--
Brad Langhorst
langho...@neb.com<mailto:langho...@neb.com>
978-380-7564
________________________________
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for the use of the addressee(s). If you are not the intended recipient, please
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in this e-mail. You should carry out your own virus checks before opening the
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are not the intended recipient, you are not authorized to use or disclose this
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delete the original message from your mail system.
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