ATAC-seq quality filtering

Question

[Rafael Soler]

Hello, I am new with the ATAC-seq analysis. I am performing now the quality controls and I wanted to know if I am doing all the necessary steps. Also could be that I am filtering the data to much and losing information:

Filtering mt reads and chloroplast

Remove PCR duplicates (Picard)

Remove multimapping alignments (MAPQ > 30)

Remove duplicates and staying only with properly paired (with samtools Flags -F 1804 -f 2)

TN5 shifting

BlackList Encode Genes

ATACseqQC (r Package)

Thank you!!