How To Process Large Chipseq Data?
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14.5 years ago
nikulina ▴ 300

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)

chip-seq • 3.6k views
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CisFinder is for motif identification, not peak calling, which is what you seem to want. Start by looking at this topic

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14.5 years ago
User 59 13k

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

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

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14.4 years ago
Ian 6.1k

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.

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