Chip-Chip Analysis Tools?

Question

[Ian]

I used to run a lot of Affymetrix based ChIP-chip analysis using MAT, but this was 2-3 years ago.

Is there now any alternative software that is (i hate to say it) better than MAT?

Thanks!

Answer 1

[Gjain]

You can try COCAS

CoCAS is a standalone Chromatin immunoprecipitation microarray (ChIP-on-chip) analysis application. It has been designed to be used primarily on Agilent microarrays scanned with an Agilent scanner. CoCAS is free software and builds upon existing packages in Java and R programming languages, notably BioConductor. CoCAS uses Java for user graphical interface, and R for the bulk of the calculations.

Here is a quick start guide.

I hope this helps.

[Ian]

Thanks, but i would like native handling of Affymetrix data.

Answer 2

[Nibua]

You have also Cisgenome http://www.biostat.jhsph.edu/~hji/cisgenome/ For ChIP on chip Tilemap is used (old but works fine). If you are on Windows you can use a graphic UI. In addition it was made for Affymetrix data.

Hope this helps