SOLID to fastq for Bowtie

classic Classic list List threaded Threaded
3 messages Options
Reply | Threaded
Open this post in threaded view
|

SOLID to fastq for Bowtie

Shalabh Sharma-2
Hi,
      I am trying to implement a SOLID pipeline for my solid data.
I really like the pipeline used in Galaxy, I was looking for conversion of SOLID to fastq, but it didn't say that how it is achieved in Galaxy.
I know for bwa you can use solid2fasta.pl but for bowtie i did not find any program or information.
I would really appreciate if you can help me with this, like how it is achieved and where i can download the program used by Galaxy.

Thanks
Shalabh Sharma
-----------------------------


Shalabh Sharma
Scientific Computing Professional Associate (Bioinformatics Specialist)
Department of Marine Sciences
University of Georgia
Athens, GA 30602-3636

___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/
Reply | Threaded
Open this post in threaded view
|

Re: SOLID to fastq for Bowtie

Jen Hillman-Jackson
Hello Shalabh,

Galaxy is open source and available here:
http://bitbucket.org/galaxy/galaxy-central/src/

Check under tools to find:
tools/fastq/fastq_groomer.py/.xml

Other SOLiD specific tools are under:
tools/solid_tools/

The rest is organized in this same general way.
This wiki may be helpful:
http://galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax

Hopefully this helps. Next time, you can just send to one list, and for
development questions, the best list would be [hidden email].
http://galaxyproject.org/Support

Best,

Jen
Galaxy team

On 8/10/11 11:23 AM, Shalabh Sharma wrote:

> Hi,
> I am trying to implement a SOLID pipeline for my solid data.
> I really like the pipeline used in Galaxy, I was looking for conversion
> of SOLID to fastq, but it didn't say that how it is achieved in Galaxy.
> I know for bwa you can use solid2fasta.pl but for bowtie i did not find
> any program or information.
> I would really appreciate if you can help me with this, like how it is
> achieved and where i can download the program used by Galaxy.
>
> Thanks
> Shalabh Sharma
> -----------------------------
>
>
> Shalabh Sharma
> Scientific Computing Professional Associate (Bioinformatics Specialist)
> Department of Marine Sciences
> University of Georgia
> Athens, GA 30602-3636
>
>
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
>    http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
>    http://lists.bx.psu.edu/

--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org/Support
___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/
Jennifer Hillman-Jackson
http://galaxyproject.org
Reply | Threaded
Open this post in threaded view
|

Re: SOLID to fastq for Bowtie

Anton Nekrutenko
Shalabh:

To add to Jen's reply bowtie supports SOLiD csfasta and QUAL files natively. However, Galaxy has a tool for converting SOLiD output to fastq here:

http://bit.ly/pXw3Ic

Tx,

anton
galaxy team




Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org



On Aug 10, 2011, at 4:09 PM, Jennifer Jackson wrote:

> Hello Shalabh,
>
> Galaxy is open source and available here:
> http://bitbucket.org/galaxy/galaxy-central/src/
>
> Check under tools to find:
> tools/fastq/fastq_groomer.py/.xml
>
> Other SOLiD specific tools are under:
> tools/solid_tools/
>
> The rest is organized in this same general way.
> This wiki may be helpful:
> http://galaxyproject.org/Admin/Tools/Tool%20Config%20Syntax
>
> Hopefully this helps. Next time, you can just send to one list, and for development questions, the best list would be [hidden email].
> http://galaxyproject.org/Support
>
> Best,
>
> Jen
> Galaxy team
>
> On 8/10/11 11:23 AM, Shalabh Sharma wrote:
>> Hi,
>> I am trying to implement a SOLID pipeline for my solid data.
>> I really like the pipeline used in Galaxy, I was looking for conversion
>> of SOLID to fastq, but it didn't say that how it is achieved in Galaxy.
>> I know for bwa you can use solid2fasta.pl but for bowtie i did not find
>> any program or information.
>> I would really appreciate if you can help me with this, like how it is
>> achieved and where i can download the program used by Galaxy.
>>
>> Thanks
>> Shalabh Sharma
>> -----------------------------
>>
>>
>> Shalabh Sharma
>> Scientific Computing Professional Associate (Bioinformatics Specialist)
>> Department of Marine Sciences
>> University of Georgia
>> Athens, GA 30602-3636
>>
>>
>> ___________________________________________________________
>> The Galaxy User list should be used for the discussion of
>> Galaxy analysis and other features on the public server
>> at usegalaxy.org.  Please keep all replies on the list by
>> using "reply all" in your mail client.  For discussion of
>> local Galaxy instances and the Galaxy source code, please
>> use the Galaxy Development list:
>>
>>   http://lists.bx.psu.edu/listinfo/galaxy-dev
>>
>> To manage your subscriptions to this and other Galaxy lists,
>> please use the interface at:
>>
>>   http://lists.bx.psu.edu/
>
> --
> Jennifer Jackson
> http://usegalaxy.org
> http://galaxyproject.org/Support
> ___________________________________________________________
> The Galaxy User list should be used for the discussion of
> Galaxy analysis and other features on the public server
> at usegalaxy.org.  Please keep all replies on the list by
> using "reply all" in your mail client.  For discussion of
> local Galaxy instances and the Galaxy source code, please
> use the Galaxy Development list:
>
> http://lists.bx.psu.edu/listinfo/galaxy-dev
>
> To manage your subscriptions to this and other Galaxy lists,
> please use the interface at:
>
> http://lists.bx.psu.edu/


___________________________________________________________
The Galaxy User list should be used for the discussion of
Galaxy analysis and other features on the public server
at usegalaxy.org.  Please keep all replies on the list by
using "reply all" in your mail client.  For discussion of
local Galaxy instances and the Galaxy source code, please
use the Galaxy Development list:

  http://lists.bx.psu.edu/listinfo/galaxy-dev

To manage your subscriptions to this and other Galaxy lists,
please use the interface at:

  http://lists.bx.psu.edu/