ATAC-QC fragSizeDist function
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Shuang He • 0
@shuang-he-16892
Last seen 2.2 years ago
China/Beijing

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!

ATAC-seq ATACseqQC • 280 views
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Julie Zhu ★ 4.3k
@julie-zhu-3596
Last seen 10 weeks ago
United States

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

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