Heat map with position
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6.5 years ago
9606 ▴ 330

Dear all,

In many publications I have found picture such as the one below, where the intensity of some chip-seq signals is shown in a range interval around a given point. For example, in the attached picture the authors show histone modification close to TSS.

However, I do not know what tool they used to do so. Can someone provide some reference?

ChIP-Seq visualization • 1.7k views
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6.5 years ago
Ido Tamir 5.2k

There are now many packages/programs that do this. If you don't want to deal with the command line I would suggest seqminer. Its in java and very easy to use - I hope they put the source code out once, because its not maintained:

http://bips.u-strasbg.fr/

Other for command line:

http://homer.salk.edu/homer/chipseq/heatmap.html

https://pythonhosted.org/metaseq/example_session.html

ngsplot

https://deeptools.github.io/

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regarding deepTools - if you check out the deepTools Galaxy instance at http://deeptools.ie-freiburg.mpg.de/, you can a) avoid the command line and b) see a youTube video on how to make a heatmap

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