Re: FW: problem using Depth of Coverage (GATK)

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Re: FW: problem using Depth of Coverage (GATK)

Jen Hillman-Jackson
Hi Gema,

The histogram tool has the columns labeled on the tool's form - there are a few different values that you could pull out and graph, using others as labels, but last one is the coverage for that region of the chrom. The second tool's output is a bedGraph file, the format is also defined on the tool form, with the last value being coverage, the full specification is also here:
http://wiki.galaxyproject.org/Learn/Datatypes#BedGraph

The tool group "Graph/Display Data" maybe of interest, or you could use a browser to visualize the bedGraph file. The resulting dataset will have links.

Best,

Jen
Galaxy team

On 4/12/13 7:20 AM, Gema Sanz Santos wrote:
Hi Jennifer,

Thank you very much for your answer.

I think that alternative is good for me, but how can I get the plot? The output is a table but I don't know exactly which columns to select for getting the histogram plot or the bed graph.

Best,
Gema

From: Jennifer Jackson <[hidden email]>
Date: Tuesday, April 9, 2013 10:50 PM
To: Gema Sanz Santos <[hidden email]>
Cc: <[hidden email]>
Subject: Re: [galaxy-user] problem using Depth of Coverage (GATK)

Hello Gema,

The tool group "GATK-Tools (beta)" is not indexed to function with the hg19 genome.

As an alternative on the public Main Galaxy server, please see the tool group " BEDTools". There are two tools here that calculate coverage using BAM data as input.

Another alternative is to set up either a local or cloud Galaxy, obtain the hg19 indexes from GATK, then run the analysis there. If you wish to try this please see:
http://getgalaxy.org
http://usegalaxy.org/cloud

Take care,

Jen
Galaxy team

On 4/7/13 11:41 PM, Gema Sanz wrote:

Hello, I´m trying to use depth of coverage to check the coverage of my reads. I already have the bam files (created with sam to bam) but they are still not recognized by depth of coverage and I got this error message:

"Sequences are not currently available for the specified build"

I used "human (homo sapiens) hg19 full" for mapping but I can´t select it, it only allows b37 version. I tried to change the build in edit parameters to b37 and then it is recognized but I got another error at the end of the analysis.

Any suggestions?

Thank you very much in advance

Gema

 



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-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
http://galaxyproject.org

-- 
Jennifer Hillman-Jackson
Galaxy Support and Training
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.  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/

To search Galaxy mailing lists use the unified search at:

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Jennifer Hillman-Jackson
http://galaxyproject.org