Roadmap Epigenomics looks random

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3.9 years ago

christoph.neu ▴ 10

Hello,
I want to analyze the differences of histone peaks between cell types. For that i obtained some bed files from the Roadmap Epigenomics project. However the data looks highly unspecific and covers mostly everything. Here is an example file and where i got it from.

For illustration I added a screenshot from IGV with H3M4me3 (a promotor mark).

The blue tracks are from roadmap the red are H3K4me3 marks (mouse) from my lab (most of the red marks overlap with TSS

I don't really know whats wrong, whether I used the wrong data source with unprocessed/filtered bed files (but if so, are there filtered ones?) or if this is correct (but if so, how could anything be concluded from that data).

ChIP-Seq • 636 views

ADD COMMENT • link updated 3.9 years ago by GenoMax 142k • written 3.9 years ago by christoph.neu ▴ 10

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Are you viewing the data with wrong genome/genome build in IGV? Looks like you have mm10 genome selected in the screenshot you posted. But this data is human correct?

ADD REPLY • link 3.9 years ago by GenoMax 142k

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Yes I do (because the data set from my lab is mm10 and this is what I had laying around), however this does not change the overall coverage of the roadmap data. The complete genome looks like this section. So even with the correct reference one would not see an enrichment at the TSS.

ADD REPLY • link 3.9 years ago by christoph.neu ▴ 10

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