I m quoting this paper figure, figure B where they write

"B) Violin plots for the normalized ATAC-seq tag density for all peaks within the indicated OC/CO groups at the indicated time points. Data were converted to a Z score based on the row-wise SD for each peak. ∗p < 0.01 Mann-Whitney U test."

My question is where is this tag density information coming from.

So far for chipseq data what I have done is

  • Aligned the data
  • Then all required data processing post alignment
  • Generated bed and bigwig files of respective samples required for comparison
  • Made tag-directory using homer.
  • Then peak-calling using homer,annotated peak using homer.

Now so far I am not able to figure out where is this tag-density information is .

Any help or suggestion would be really appreciated.


1 Answer 1


You can use Homer to retrieve tag densities, quoting from their manual:

Calculating ChIP-Seq Tag Densities across different experiments

annotatePeaks.pl is [a] useful program for cross-referencing data from multiple experiments. In order to count the number of tags from different sequencing experiments, you must first create tag directories for each of these experiments. Once created, tag counts from these directories in the vicinity of your peaks can be added by specifying "-d ...". You can specify as many tag directories as you like. Tag totals for each directory will be placed in new columns starting on column 18. For example:

annotatePeaks.pl pu1peaks.txt mm8 -size 400 -d Macrophage-PU.1/ Bcell-PU.1/ > output.txt

  • $\begingroup$ Out of curiosity, what is actually? Reads per base pair? $\endgroup$
    – StupidWolf
    Oct 23, 2019 at 10:51
  • $\begingroup$ @StupidWolf, I cannot seem to understand the question, could you please provide more context? $\endgroup$
    – haci
    Oct 23, 2019 at 11:01
  • $\begingroup$ Sorry @haci typed too fast, I meant what is "tag density" exactly. I don't use Homer, so when I read the publication pointed out in the original question, I assume it's something like reads per bp of the peak? $\endgroup$
    – StupidWolf
    Oct 23, 2019 at 11:03
  • 1
    $\begingroup$ In my understanding it is the number of reads in a given genomic region or peak, in that respect it would be analogous to gene counts. I also found a similar Q&A on this: $\endgroup$
    – haci
    Oct 23, 2019 at 11:11
  • $\begingroup$ I finally landed up here homer.ucsd.edu/homer/ngs/quantification.html $\endgroup$
    – kcm
    Oct 23, 2019 at 11:31

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