visualization of coverage for ATAC seq --- bam or bigwig
Entering edit mode
17 months ago

Hi all,

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:

Coverage track by Givz

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.

Genrich ATAC-seq coverage tracks Gviz • 1.3k views

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