I am new to ATACseq data. Earlier, I have processed mainly RNAseq and few Chip seq data, thus i used same tools for atacseq as well.
I used STAR (default parameters plus --outSAMstrandField intronMotif) to generate bam and wig files, then I used macs2 (-B -q 0.01) to call peak using those bam files.
Is this a correct way to process? Also, can you recommend a tool to get the differential peaks from this ATACseq data?