Re: [galaxy-user] ChIP-Seq Normalization to total number of reads

2013-12-02 Thread Björn Grüning 
Hi Catheryn,

for ChIP-seq analysis, normalisation and BAM file correlation we use
deeptTools. Here you can read more about it:

https://github.com/fidelram/deepTools

And here is the toolshed repository:
http://toolshed.g2.bx.psu.edu/view/bgruening/deeptools

Cheers,
Bjoern

 Dear Galaxy,
 
  
 
 I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I
 have 2 datasets that I want to compare after normalizing each of them
 to their respective inputs, and these 2 datasets have very different
 number of reads to start with, is there a way to first normalize each
 dataset to total number of reads in Galaxy?
 
  
 
 Thanks. Your help is very much appreciated.
 
  
 
 Catheryn
 
 
 
  
 
 
 ___
 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:
 
   http://galaxyproject.org/search/mailinglists/



___
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:

  http://galaxyproject.org/search/mailinglists/

[galaxy-user] ChIP-Seq Normalization to total number of reads

2013-12-01 Thread Wooi Lim 
Dear Galaxy,

I am trying to analyze my ChIP-Seq data from Illumina using Galaxy. I have 2 
datasets that I want to compare after normalizing each of them to their 
respective inputs, and these 2 datasets have very different number of reads to 
start with, is there a way to first normalize each dataset to total number of 
reads in Galaxy?

Thanks. Your help is very much appreciated.

Catheryn



___
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:

  http://galaxyproject.org/search/mailinglists/