How To Process Large Chipseq Data?

Question

[nikulina]

Good afternoon!

I have a question concerning processing of large (~800 mb) raw Chipseq data . I have found CisFinder, but it is effective with sequences up to 50 Mb. Could you advise any tools (for windows) that will allow me to obtain peak coordinates?

Thank you in advance.

(The data of interest are here)

[Mikael Huss]

CisFinder is for motif identification, not peak calling, which is what you seem to want. Start by looking at this topic

Answer 1

[User 59]

If you want to process ChiP-Seq data with BioConductor there are slides and and a case study on the BioConductor website.

[Stew]

This course manual also gives a good overview of using R for chIP-seq analysis.

Answer 2

[Ian]

You could try CisGenome, which has a user friendly GUI. I have not personally used it as I favour Linux-based solutions like MACS. You could look into a UNIX emulator for Windows, e.g. Cygwin.