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.eshttp://www.cabimer.es/ http://www.cabimer.es/web/es/unidades-apoyo/genomica
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:****
- 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
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:
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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:****
- 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
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:
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:
galaxy-user@lists.galaxyproject.org
-
Abhay Krishna -
Mónica Pérez Alegre -
shamsher jagat