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. 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/
>
-- 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
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/
