Question: Tissue-specific Histone Mark bam files?
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gravatar for epaminonda
8 months ago by
epaminonda10
United Kingdom
epaminonda10 wrote:

Hi everybody

A colleague has developed a machine learning tool to perform enhancer prediction based on histone mark ChIP-seq data.

I would like to test the tool by performing enhancer calling in a tissue-specific fashion, and I'm looking for publicly available histone modification ChIP-seq data. If possible I'm hoping to find bam/sam alignments as the tool seems to require them. I believe wig/bigWig/bigBed tracks will not work.

Are there any such datasets? I have started looking at ENCODE and Roadmap Epigenomics data, but I'm having difficulty finding bam files for the data. For the Roadmap Epigenomics project, I did find .bed files of the alignments, which means I could theoretically generate bam files with bedtools. Is this my only option?

In genera, if somebody knows the location/availability of tissue specific histone ChIP-seq bam tracks that would be really appreciated.

ADD COMMENTlink modified 8 months ago • written 8 months ago by epaminonda10
0
gravatar for epaminonda
8 months ago by
epaminonda10
United Kingdom
epaminonda10 wrote:

Answering some of my own questions -

I found the following portal to be quite useful to assess availability of tissue specific histone mark data

Cistrome DB

It seems to return results coming from both large scale studies (ENCODE+Roadmap Epigenomics) and small studies (focusing on, say, a few histone marks for a selected tissue of interest)

ADD COMMENTlink written 8 months ago by epaminonda10
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