Question

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

ADD COMMENT • link updated 6.3 years ago by Ram 44k • written 14.5 years ago by nikulina ▴ 300

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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

ADD REPLY • link updated 5.3 years ago by Ram 44k • written 14.5 years ago by Mikael Huss 4.8k

Ram · Answer 1 · 2010-06-22

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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.

ADD COMMENT • link updated 6.3 years ago by Ram 44k • written 14.5 years ago by User 59 13k

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

ADD REPLY • link updated 6.3 years ago by Ram 44k • written 14.5 years ago by Stew ★ 1.4k

Ram · Answer 2 · 2010-07-02

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14.5 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.

ADD COMMENT • link updated 6.3 years ago by Ram 44k • written 14.5 years ago by Ian 6.1k