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/
