I m quoting this paper , 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.