I dont think Cistrome can provide sufficient visualization options. In CEAS analysis it can provide overall picture of genome binding regions or some relative binding histograms. I beleive what Monica is asking when one has chip enriched regions how to visualize such selected regions- I will suggest IGV or loading file to UCSC genome browser. However It will be interesting if either some one from Galaxy/ Cistrome (Tau/ Shirley) can add to this post as personally it may be easy to do everything in cistrome/ Galaxy rather then flipping files between various tools. 

Best

2011/11/16 Abhay Krishna <abhay.krishna@gmail.com>
I think closest to what you want to do in galaxy can be done in cistrome

http://wiki.g2.bx.psu.edu/Community/Cistrome


Unless I am missing some galaxy tool in testing, which other galaxy users more closely following galaxy test can comment on

best
Abhay



2011/11/16 Mónica Pérez Alegre <monica.perez@cabimer.es>

Hi all

 

We are working with chip-chip data of S. cerevisiae (from Affymetrix) and actually we have two problems and we don´t know if it´s possible to perform in Galaxy:

 

  1. We use the tool intersect to get the annotation of positive genomic regions in our file bed. After, we need calculate statistical enrichments for associations between genomics regions and annotations. It´s this possible in Galaxy?
  2. Other query. How plot for visual inspection enrichment ratio profile versus different sets of genomic loci (i.e.: tRNA, LTR,…)

 

Best Regards,

 

☺If you have used the Services of the Genomics Unit of Cabimer, we would be grateful if you would give us a mention in future publications

Mónica Pérez Alegre, PhD

Genomics Unit

CABIMER-CSIC

Edif. CABIMER - Avda. Américo Vespucio s/n

Parque Científico y Tecnológico Cartuja 93

41092 Seville-SPAIN

Tlf:   +34 954 467 828

Fax: +34 954 461 664

www.cabimer.es

http://www.cabimer.es/web/es/unidades-apoyo/genomica

 


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___________________________________________________________
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
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 http://lists.bx.psu.edu/listinfo/galaxy-dev

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