[galaxy-user] RV: Visual and Conputational Analysis of positive sites in chip-chip data

[shamsher jagat]

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 at 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 at 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*<http://www.cabimer.es/web/es/unidades-apoyo/genomica>
>> ****
>>
>> ** **
>>
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