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Old 09-24-2013, 08:42 PM   #1
Junior Member
Location: Seoul, Korea

Join Date: Sep 2013
Posts: 1
Default How visualize the BS-seq profiles?

Hi, I'm newbee for NGS, especially BS-seq,
though my PI think I should be able to manipulate the data.

I have good qual BS-seq data, and I could map the the data with
BS-seq-specialized tools, such as BISMARK etc.

Though I could not visualize any general data what found from several papers.
(Specially for methylation profiles around genes or TE; DMR peak calculation (not DMC))

Do you have any recommendations ?
I am slightly available for R; though no sufficient tools was found.

hope for your good days.
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Old 09-25-2013, 12:20 AM   #2
Simon Andrews
Location: Babraham Inst, Cambridge, UK

Join Date: May 2009
Posts: 871

You can certainly construct these kinds of plot in SeqMonk. There's a tutorial video here which goes through the process of constructing a methylation trend plot.

I'm not aware of a tool which directly supports this sort of plot in R, but you could make something out of the core R components relatively easily by just tiling graphs togehter.
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