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 <j...@bx.psu.edu <mailto:j...@bx.psu.edu>>
Date: Tuesday, April 9, 2013 10:50 PM
To: Gema Sanz Santos <ge2sa...@gmail.com <mailto:ge2sa...@gmail.com>>
Cc: <galaxy-user@lists.bx.psu.edu <mailto:galaxy-user@lists.bx.psu.edu>>
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:
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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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