Lali:

In your case the workflow for capture re-sequencing should look like this:

1. QC data (groom fastq files and plot quality distribution)
2. Map the reads (use bwa)
3. Generate and filter pileup 
4. Intersect pileup with coordinates of sure select bates. 

However, before you dive in please understand basic Galaxy functionality by 
taking a look at http://usegalaxy.org/galaxy101 and watching *all* 
Illumina-related Galaxy quickies (black boxes on the front page on Galaxy). 
Next, take a look at http://usegalaxy.org/heteroplasmy.

Note, that we are working on bringing "industrial-strength" diploid genotyping 
functionality in Galaxy in the next two-three months that will include more 
sophisticated genotypers, recalibration and realignment tools, and novel 
visualization approaches.

Thank for using Galaxy.

anton
galaxy team  



On Apr 5, 2011, at 2:44 AM, Lali wrote:

> Hi!
> I am having problems with my sequencing results, but I am a newbie at this; 
> so I am thinking there is something wrong with my analysis. So far, I've 
> tried Galaxy and CLC Workbench, but with CLC I could not align to the whole 
> genome, only to individual chromosomes (maybe there is a way, but by the time 
> the trial ended I had not found it).
> 
> I used SureSelect capture kit and did single end sequencing on an Illumina. 
> The files the lab sent me are FastQ Illumina 1.5 files, my samples were 
> indexed, and I got a series of files each representing an Index.
> 
> What would be the standard workflow for this kind of data?
> Which tools/settings?
> 
> Does anyone have an example Galaxy workflow for preparing (clipping adapters, 
> quality trimming) and mapping Targeted Resequencing Data?
> 
> Is there a way to obtain a coverage report through Galaxy?
> 
> Is it possible to ignore/discard the reads mapped when the coverage is below 
> a certain threshold?
> 
> I know, I know, a lot of things, but I am very lost.
> Any help is appreciated.
> 
> L ___________________________________________________________
> The Galaxy User list should be used for the discussion of
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Anton Nekrutenko
http://nekrut.bx.psu.edu
http://usegalaxy.org




___________________________________________________________
The Galaxy User list should be used for the discussion of
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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:

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