Question: Searching for genomic coordinates of histone/chromatin states in Roadmap epigenomics
0
gravatar for CL
12 weeks ago by
CL0
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, https://egg2.wustl.edu/roadmap/web_portal/processed_data.html#ChipSeq_DNaseSeq 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: https://egg2.wustl.edu/roadmap/data/byFileType/peaks/consolidated/gappedPeak/

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).

Thanks!

chip-seq • 118 views
ADD COMMENTlink written 12 weeks ago by CL0
1

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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