differential ATAC-seq peak analysis using dpeak

[Dhurjhoti Saha]

Hi all,

I want to perform differential analysis of ATAC seq 'nfr' peaks. Kindly suggest me the best way to do this.

I have tried to use the 'dpeak' option however ended up with more than 200,000 differential nfr peaks. I have followed the following example to do the differential analysis -

Example 2. Compare H3K4me3 ChIP-Seq data between two samples A and B,  each sample has its own input effect to be subtracted.

python danpos.py dpeak H3K4me3_sampleA:H3K4me3_sampleB.bed.gz     -b H3K4me3_sampleA:input_sampleA,H3K4me3_sampleB.bed.gz:input_sampleB

I had used the mono-nucleosme file as a control file and nfr files as sample files.

Thanks in advance!

If anyone needs any more details, let me know.