I am working with ATAC-seq datasets and follow a pipeline with:
FastQC---Cutadapt---FastQC---Bowtie2---Filter "properly mapped reads" (samtools -F 1804)---merge filtered BAM files by cell type----Genrich(-j -e chrM -E encodeblacklist -r -m 30 -f)
I wonder what files should I use for visualization of coverage track of the data--- merged BAM files or BigWig files converted from Genrich output Bedgraph-ish files ? It seems different for pair end sequence data which is discussed before ATACseq visualization.
I want to plot as follows:
It is created by Gviz R package, but I am not sure which file -- BAM or Bigwig --- the coverage datatrack are built from?
BTW, any other software can I use for visualization this track ?
Welcome any suggestions ! Thank you for your help.