Integration of ATACseq, RNAseq data with ChIPseq data
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12 months ago

Hello everyone, I am experiencing some difficulties in the integration of ATACseq data with K27me3 ChIP data. Peaks were called with MACS2 --nomodel --extsize75 , broad peaks in case of ChIP data, for ATACseq they were narrow peaks. So after summarizeOverlaps counts and DeSEQ2 analysis for ATAC and K27me3 separately the significant regions of ATAC do not overlap with regions of K27me3. It might be a biological effect. However, a similar analysis of RNAseq and H3K4me3 overlap also didn't reveal overlap in significant regions. This is very weird because I would expect gene expression to overlap with H3K4me3 like 90%. How to interpret such a result? Should I do summarizeOverlap counts with ATAC or RNAseq and ChipSeq altogether from the beginning? Many thanks in advance, Anna

ChIP-Seq integration • 431 views
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So after summarizeOverlaps counts and DeSEQ2 analysis for ATAC and K27me3 separately the significant regions of ATAC do not overlap with regions of K27me3.

What to say about this? Maybe this is the biology. More details are needed. Species, setup, celltype, and code.

However, a similar analysis of RNAseq and H3K4me3 overlap also didn't reveal overlap in significant regions.

How did you do the overlap? Promoters of DEGs with the differential peaks?

How to interpret such a result?

Not possible without details.

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Thank you ATpoint for your reply. I am just struggling on how to integrate the ATACseq and ChIPseq in the best possible way. Do you know how to do this? The overlap of RNAseq was indeed done with DEG and the annotation of differential peaks. So, as a result, low expressed RNA genes are correlating with H3K4, but this is not what I would expect... I would appreciate any suggestions about this topic. PS I already figured out that indeed K27me3 is generally overlapping with closed ATAC regions and bivalent promoters (with ChromHMM).

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