ATAC-seq quality filtering
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!!
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Rafael Soler •
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