Question: How to perform analysis for repetitive elements in ATAC-Seq data?
gravatar for Deepak Tanwar
6 months ago by
Deepak Tanwar4.1k
ETH Zürich, Switzerland
Deepak Tanwar4.1k wrote:


I have questions about performing repeat-elements (RE) analysis in ATAC-Seq data.

So, I have RE information from repeatmasker

RE elements table screenshot

Now, I have bam files from ATAC-Seq.

I think I have 2 approaches to know which repeat-elements have less or more chromatin accessibility (depending on how I want to look at the RE):

  1. Read the counts in the windows of each RE transcript and perform differential analysis.
  2. Read the counts at the sub-family level and perform differential analysis.


Is my approach correct, statistically?

atac-seq repeat-elements • 279 views
ADD COMMENTlink modified 6 months ago • written 6 months ago by Deepak Tanwar4.1k

Out of interest, can you map reads uniquely to these repeats? I imagine you have a lot of multimappers and therefore only few uniquely / reliable alignments to them, and by this a sparse matrix of counts?

ADD REPLYlink modified 6 months ago • written 6 months ago by ATpoint46k

I do not have a sparse matrix for ATAC-Seq data. After filtering out the RE with low counts, I still left with approx. 1.5M RE. I did not filter out reads with MAPQ less than 30.

But, for RNA-Seq, one has to allow for multi-mapping.

For point number 2 in my question:

ADD REPLYlink written 6 months ago by Deepak Tanwar4.1k
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