Rv: Visual And Conputational Analysis Of Positive Sites In Chip-Chip Data

Question: Rv: Visual And Conputational Analysis Of Positive Sites In Chip-Chip Data

7.0 years ago by

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

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modified 7.0 years ago by Abhay Krishna • 70 • written 7.0 years ago by Mónica Pérez Alegre • 60

7.0 years ago by

Abhay Krishna • 70

Abhay Krishna • 70 wrote:

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>

ADD COMMENT • link written 7.0 years ago by Abhay Krishna • 70

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>

ADD REPLY • link written 7.0 years ago by shamsher jagat • 590

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