Chip-Seq and correlation of bam file

Question

[qudrat.nii]

I want to compare replicates, I calculated read counts over each bin (5 kilobases (kb)) across the whole genome using these commands:

bedtools makewindows -g hg38.fa.txt -w 5000 >hg38.5Kb.windows.bed
bedtools intersect -a hg38.5Kb.windows.bed -b sample1.sorted.bam -c -sorted >sample1.5Kb.windows.counts.bedg

Now, I want to calculate the reads per million values for each bin to calculate the Spearman correlation coefficient.

Please guide me

Answer 1

[jared.andrews07]

Use deepTools' plotCorrelation function.

[qudrat.nii]

I need value not the plot

[jared.andrews07]

Yes, which are also output to file by the function. Please read their example.