Re: [galaxy-user] Generating pileup for SNP analysis

2011-02-22 Thread Jennifer Jackson 

Hello Christine,

We have confirmed that the reads have Sanger qual format, not Illumina 
(as were originally run in your history) or Solexa (as some are at NCBI, 
from other SRA projects, but not this one). Please re-run the Fastq 
groomer with Sanger as the input type and all should run correctly.


Thank you again for working with us to resolve the issue and for using 
Galaxy! Please let us know if we can help more or if the results after 
the re-run are not what you expect.


Best,

Jen
Galaxy team

On 2/11/11 7:20 AM, Christine Picard wrote:

I am a new user to Galaxy, and I was hoping someone might be able to
help with this small problem.  I am using Drosophila resequencing data
downloaded from the SRA and trying to look for SNPs that differentiate
the two strains.  I've gotten as far as generating the pileup for each
strain, but my column which has the consensus base is always an N.  Can
anyone help me out?

thanks, Christine

--
Christine J. Picard, Ph.D.
Postdoctoral Research Associate
Department of Entomology
Texas A&M University
TAMU 2475
College Station, TX
77843-2475
christine.pic...@gmail.com 



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--
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http://usegalaxy.org
http://galaxyproject.org
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Re: [galaxy-user] Generating pileup for SNP analysis

2011-02-22 Thread Jennifer Jackson 

Hello Christine,

The data issue goes back to the initial grooming step. When using "Fastq 
Groomer", choose "Solexa" instead of "Illumina 1.3+" as the Input FASTQ 
quality score type. This preserves the correct quality score 
translation, which was the root of the problem in the derivative steps.


Hopefully this helps when you do the re-run of the analysis, but please 
let us know if we can help more. I'll send you a link off-line to a 
history with some more specific information to your project,


Thanks,

Jen
Galaxy team



On Wed, Feb 16, 2011 at 9:10 AM, Jennifer Jackson mailto:j...@bx.psu.edu>> wrote:

Hi Christine,

Would you like to share a link to your history? Use Options -> Share
or Publish and we can take a look at the input data (likely the
source of problem).

Best,

Jen
Galaxy team


On 2/11/11 7:20 AM, Christine Picard wrote:

I am a new user to Galaxy, and I was hoping someone might be able to
help with this small problem.  I am using Drosophila
resequencing data
downloaded from the SRA and trying to look for SNPs that
differentiate
the two strains.  I've gotten as far as generating the pileup
for each
strain, but my column which has the consensus base is always an
N.  Can
anyone help me out?

thanks, Christine

--
Christine J. Picard, Ph.D.
Postdoctoral Research Associate
Department of Entomology
Texas A&M University
TAMU 2475
College Station, TX
77843-2475
christine.pic...@gmail.com 
>



___
The Galaxy User list should be used for the discussion of Galaxy
analysis and
other features on the public server at usegalaxy.org
.  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




--
Christine J. Picard, Ph.D.
Postdoctoral Research Associate
Department of Entomology
Texas A&M University
TAMU 2475
College Station, TX
77843-2475
christine.pic...@gmail.com 



--
Jennifer Jackson
http://usegalaxy.org
http://galaxyproject.org
___
The Galaxy User list should be used for the discussion
of Galaxy analysis and other features on the public
server at usegalaxy.org. 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

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Galaxy lists, please use the interface at:

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Re: [galaxy-user] Generating pileup for SNP analysis

2011-02-16 Thread Jennifer Jackson 

Hi Christine,

Would you like to share a link to your history? Use Options -> Share or 
Publish and we can take a look at the input data (likely the source of 
problem).


Best,

Jen
Galaxy team

On 2/11/11 7:20 AM, Christine Picard wrote:

I am a new user to Galaxy, and I was hoping someone might be able to
help with this small problem.  I am using Drosophila resequencing data
downloaded from the SRA and trying to look for SNPs that differentiate
the two strains.  I've gotten as far as generating the pileup for each
strain, but my column which has the consensus base is always an N.  Can
anyone help me out?

thanks, Christine

--
Christine J. Picard, Ph.D.
Postdoctoral Research Associate
Department of Entomology
Texas A&M University
TAMU 2475
College Station, TX
77843-2475
christine.pic...@gmail.com 



___
The Galaxy User list should be used for the discussion of Galaxy analysis and
other features on the public server at usegalaxy.org.  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
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other features on the public server at usegalaxy.org.  For discussion of local
Galaxy instances and the Galaxy source code, please use the Galaxy Development
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[galaxy-user] Generating pileup for SNP analysis

2011-02-11 Thread Christine Picard 
I am a new user to Galaxy, and I was hoping someone might be able to help
with this small problem.  I am using Drosophila resequencing data downloaded
from the SRA and trying to look for SNPs that differentiate the two strains.
 I've gotten as far as generating the pileup for each strain, but my column
which has the consensus base is always an N.  Can anyone help me out?

thanks, Christine

-- 
Christine J. Picard, Ph.D.
Postdoctoral Research Associate
Department of Entomology
Texas A&M University
TAMU 2475
College Station, TX
77843-2475
christine.pic...@gmail.com
___
The Galaxy User list should be used for the discussion of Galaxy analysis and
other features on the public server at usegalaxy.org.  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/