I tried ATAC-QC package For the fragSizeDist function, I wonder that whether the input bam file need to be the raw bam files which include the chrM, duplicates. When I tried to input the bam file (q30) which was removed the adapters,duplicates, chrM, the fragment distribution seemed a little strange since the number of fragment < 100bp (which was considered as nucleosome free region) was similar with around 200bp.

The duplication rate is 34%, the %chrM of filtered bam is 50%.

Thank you in advance!

Shuang, It seem that your library contains a lot of mitochondria DNA, which is a waste of reads. For your future reference, it is more efficient to deplete mitochondria DNA when constructing the ATAC-seq sequencing library. I am wondering what the fragment size distribution looks like (ATACseqQC::fragSizeDist) with chrM reads included in the BAM file. Best regards, Julie