Scripts and Functions related to ATACseq data analysis
FastQC Trimmomatic Bowtie2 (-X 2000 parameter)
Remove alignments that:
- map to the MT chromosome
- are duplicate as found by Picard Tools markduplicates
- have a mapq score < 30
- are non properly paired as defined by samtools 0x02 flag
Call peaks with MACS2 Differential analysis with DiffBind