9. ATAC-seq : ATAC signal file

In a final step, we will generate signal files in the bigwig format, which represent continuous signals along the genome. We will use the function bamCoverage from deepTools to acheive this.

cd 

mkdir -p analysis/bigwig/ATAC

bamCoverage \
--bam data/processed/ATACseq/Bowtie2/ATAC_REP1_aligned_filt_sort_nodup.bam \
--outFileName analysis/bigwig/ATAC/ATAC_REP1.bw \
--outFileFormat bigwig \
--normalizeUsing RPKM \
--ignoreDuplicates --centerReads \
--binSize 200 \
--numberOfProcessors 3

Look at the extra parameters from the bamCoverage, that you could possibly incorporate.

Extra challenge

Like before, visualize your ATAC bigwig file in the IGV web app.
However, try visualizing both ATAC and CTCF bigwig together with the corresponding MACS2 peak files. Can you find regions (like near gene promoters) where they overlap? What does this tell you biologically ?