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