Question: Searching for genomic coordinates of histone/chromatin states in Roadmap epigenomics
gravatar for CL
12 weeks ago by
CL0 wrote:

Hi everyone,

I am trying to get genomic coordinates for histone marks or chromatin states, preferably something like bed files (hg19), for human adult lung tissue. I have been checking in Roadmap Epigenomics project, but as I not familiar with ChIP-Seq data, I am not sure which files I should download. First, the page shows both the input data or the processed data - I assume I am looking for processed data? Then, if I go into the processed data, I can see in c.Peak calling and d.Genome-wide signal coverage tracks. I think I am aiming for c.Peak calls? In c. there is the possibility to get narrow, gapped or broad peaks. It recommends to get gapped peaks, so then I go to this link:

And I look for the ID that corresponds to lung which seems to be E096 Lung (6 trk)

[ ] E096-H3K4me1.gappedPeak.gz 31-Oct-2013 04:31 6.1M
[ ] E096-H3K4me3.gappedPeak.gz 07-Sep-2014 23:48 2.5M
[ ] E096-H3K9me3.gappedPeak.gz 31-Oct-2013 04:31 10M
[ ] E096-H3K27ac.gappedPeak.gz 31-Oct-2013 04:31 3.9M
[ ] E096-H3K27me3.gappedPeak.gz 07-Sep-2014 23:48 1.8M
[ ] E096-H3K36me3.gappedPeak.gz 31-Oct-2013 04:31 4.4M

I just want to know if my rationale is correct or if anyone has any recommendations of how to get this histone genomic coordinates for human lung tissue specifically (adult).


chip-seq • 118 views
ADD COMMENTlink written 12 weeks ago by CL0

I think that makes sense, just be aware that the gappedPeak files are in BED12+3 format.

ADD REPLYlink written 12 weeks ago by husensofteng270
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