Hello Mathew,

An an interval file of annotations and most of the tools under the group 'Operate on Genomic Intervals' can be used to annotate (find overlap with) an interval/bed file of your peaks, with the exception of the 'Profile Annotation' tool. This tool functions on certain genomes only - and not custom genomes.

Take care,

Jen
Galaxy team

On 9/11/12 5:19 AM, Mathew Bunj wrote:
Thanks Jen for a detailed explanation. One question I have is- If I run
the MACS on my pre-aligned  reads on ChIPseq data, will I be be able to
annotate my peaks from MACS either using  fetch to  closet
non-overlapping feature or profile annotation. In summary is there a way
to annotate peaks for bacterial genes under any other tool in galaxy.

Thanks

Mathew
------------------------------------------------------------------------
*From:* Jennifer Jackson <j...@bx.psu.edu>
*To:* Mathew Bunj <mathewb...@yahoo.com>
*Cc:* "galaxy-user@lists.bx.psu.edu" <galaxy-user@lists.bx.psu.edu>
*Sent:* Monday, September 10, 2012 11:32 AM
*Subject:* Re: [galaxy-user] Adding a custom genome for using MACS in Galaxy

Hello Mathew,

If you already have mapped your data, then you can just upload the
BAM/SAM dataset(s), sort if necessary, leave the database unassigned,
and run MACS. This workflow has an example of how to sort a BAM file and
send to MACS - you don't have to use this exactly, in fact the settings
(especially for MACS) are likely not appropriate. Just examine the
general sort rules and use the parts of it that make sense for your
purposes, and run the tools independently or modify to create your own
workflow:
http://main.g2.bx.psu.edu/u/jen-bx-galaxy-edu/w/sort-bam-for-peak-calling-macs-tool

If you want to convert SAM-to-BAM (not really necessary) or when
starting with raw sequence data that needs to be mapped (or find that
you want to map it again), then the reference custom genome should be
loaded along with the sequence data. Again, leave the database
unassigned for all. The general protocol is covered in #3 from the Using
Galaxy paper (make adjustments for tag size, effective genome size, etc.
as needed, using the MACS documentation linked from the tool's page as a
guide):
http://main.g2.bx.psu.edu/u/galaxyproject/p/using-galaxy-2012

To prepare, load, troubleshoot, and use a custom reference genome with
tools (such as mapping tools), please see this wiki and the links it
points to.
http://wiki.g2.bx.psu.edu/Support#Custom_reference_genome
In short, tool forms that have a custom genome option will ask "Choose
the source for the reference list:" or similar - you will select
"History" and then select the dataset where your custom reference genome
has been uploaded in fasta format and assigned the datatype "fasta". It
is very important that the chromosome/scaffold identifiers in the
reference genome and those in any other files that refer to it are
identical (in for example, a SAM or GTF dataset). This is where doing
all of the analysis within Galaxy can be sometimes easier, since our
tools maintain this internal data consistency.

This should help to get you started, but please let us know if you need
more help as the analysis proceeds,

Best,

Jen
Galaxy team

On 9/10/12 9:59 AM, Mathew Bunj wrote:
 > I have  a chipseq data which ha sbeen alined against bacterial genome. I
 > am trying to figure out how I can use peak calling MACS in Galaxy main
 > server. Do I need to use the bactaerial genome (in genome option of data
 > uplaod) in uplaoding the data. Could some one diect me if I can add my
 > own custom genome for MACS program with in Galaxy main.
 > Thanks
 >
 >
 > ___________________________________________________________
 > The Galaxy User list should be used for the discussion of
 > Galaxy analysis and other features on the public server
 > at usegalaxy.org <http://usegalaxy.org/>.  Please keep all replies on
the list by
 > using "reply all" in your mail client.  For discussion of
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 >
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 >
 > To manage your subscriptions to this and other Galaxy lists,
 > please use the interface at:
 >
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 >

-- Jennifer Jackson
http://galaxyproject.org



--
Jennifer Jackson
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
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use the Galaxy Development list:

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