Hi Rich,

Tools will allow grooming to be skipped if the data is already in fastqsanger or fastqcssanger format (as appropriate). This can be set at upload or on the "Edit Attributes" form (pencil icon). For Illumina, these would be data resulting from the CASAVA 1.8+ pipeline.


For Illumina 1.5, select "Illumina 1.3-1.7" on the FASTQ Groomer tool form to properly format the data.

Thanks for bringing up a good topic! Not having to groom can save both time and disk space.

Best,

Jen
Galaxy team

On 2/29/12 8:24 AM, Richard Mark White wrote:
I have a question about the groomer. Do all Illumina runs need to be
groomed, or are there situations where it can be skipped?? (My data says
illumina 1.5, so ive been picking input type as illumina 1.3-1.5.)

rich


------------------------------------------------------------------------
*From:* Jennifer Jackson <j...@bx.psu.edu>
*To:* Ateequr Rehman <atee...@yahoo.com>
*Cc:* "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
*Sent:* Wednesday, February 29, 2012 10:57 AM
*Subject:* Re: [galaxy-user] ILLumina 1.9 Hiseq

Hello,

The input quality score type should be set as "Sanger" for your data.

Thanks!

Jen
Galaxy team

On 2/29/12 7:39 AM, Ateequr Rehman wrote:
 > Dear Glaxy users and admin
 >
 > I ran my sequence data on FASTQC tool,
 > output says it is
 > Encoding Sanger / Illumina 1.9
 >
 > now i want to groom my file, but groomer does not have option for 1.9 in
 > "Input FASTQ quality scores type"
 >
 > any idea which option i should select to grroom my file,
 >
 > later i want to run Bowtie or Tophat,
 >
 > Thanks
 > **
 >
 >
 >
 > ___________________________________________________________
 > The Galaxy User list should be used for the discussion of
 > Galaxy analysis and other features on the public server
 > at usegalaxy.org <http://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/wiki/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 Jackson
http://usegalaxy.org
http://galaxyproject.org/wiki/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/

Reply via email to