Normalise read counts between two bam files

Question

[nanana]

I'm trying to calculate the read depth ratio between two bam files in a specific genomic region.

One of these samples was sequenced deeper than the other - what's the recommend way to normalise read counts between the two?

Deeptools seems like a great standalone option for normalising between two bam files, can anyone outline the method they use to create a scaling factor?

For example, I am interested in calculating the read depth ratio in a particular window (window1 below) normalised for sequencing depth differences between two bam files, bam1 and bam2

Total number of mapped reads in bam1: 42973364
Reads in window1 in bam1: 9359
Total number of mapped reads in bam2: 101526426
Reads in window1 in bam2: 28347

How can I calculate normalised read depth ratio in this example?

Answer 1

[ATpoint]

Have a look at deeptools bamCompare. It normalized two BAM files to each other, offering a number of normalization methods.

[nanana]

I just updated my question. I know that deep tools handles this, my question is, in the hypothetical example I give above, what is the appropriate way to calculate this by hand