Workflow assistance

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Workflow assistance

Kevin Pawlik PhD

After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following:

 

I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed Bowtie alignments. I want to find the allelic positions where the (+) genomes differ from the (-) genome.

 

Many thanks,

 

Kevin

 

 

 

 


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Re: Workflow assistance

Anton Nekrutenko
<base href="x-msg://73/">Kevin:

Is this a diploid or haploid organism?

anton
galaxy team



On Jul 12, 2011, at 11:38 PM, Kevin Pawlik PhD wrote:

After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following:
 
I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed Bowtie alignments. I want to find the allelic positions where the (+) genomes differ from the (-) genome.
 
Many thanks,
 
Kevin
 
 
 
 
___________________________________________________________
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/
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Re: Workflow assistance

Anton Nekrutenko
<base href="x-msg://73/">Kevin:

Yes, for Illumina data BWA would be the best option from what is currently available at the main site. You can then identify variants with pileup and compare across the samples much as it is shown at http://usegalaxy.org/heteroplasmy. This should give you a rough idea on what to expect. However, piplines for proper (1000genomes-like) varinat calling that include realignment and recalibration steps are coming by the end of the Summer.

Thanks!

anton

 

On Jul 13, 2011, at 1:43 PM, Kevin Pawlik PhD wrote:

Hi, Anton:
 
Diploid, 2x50 PE sequencing, rougly 5x coverage per sample. This is low coverage as a “first pass” - does that make a difference in the workflow strategy? Also, would BWA have been the better alignment option?
 
Thank you,
 
Kevin
 

From: Anton Nekrutenko [mailto:[hidden email]] 
Sent: Wednesday, July 13, 2011 9:07 AM
To: Kevin Pawlik PhD
Cc: [hidden email]
Subject: Re: [galaxy-user] Workflow assistance
 
Kevin:
 
Is this a diploid or haploid organism?
 
anton
galaxy team
 
 
 
On Jul 12, 2011, at 11:38 PM, Kevin Pawlik PhD wrote:


After viewing tutorials and reading the information associated with various tools, I ask that you point me toward an appropriate workflow for the following:
 
I sequenced (Illumina) 5 genomes of phenotype(+) samples and 1 genome of a phenotype(-) control. I uploaded fastqsanger files to Galaxy and performed Bowtie alignments. I want to find the allelic positions where the (+) genomes differ from the (-) genome.
 
Many thanks,
 
Kevin
 
 
 
 
___________________________________________________________
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/