Chip-Seq and correlation of bam file
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14 months ago
qudrat.nii ▴ 40

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

Chip-Seq • 803 views
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I need value not the plot

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

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