Hello,

This is my first post so please inform me if it's not following rules correctly.

CONTEXT:

I have 2 bigwig files. I generated them from bam files (fastq aligned with tophat then sorted by samtools), that I changed into bed files (bamToBed + awk) with extended reads. Eventually, I use bedtools genomecov + bedGraphToBigWig (UCSC tool) to obtain the bigwig files.

It might be a little fastidious but it's the way the code was designed.

QUESTION:

I want to correlate the 2 bigWig files together. I can use the UCSC bigWigCorrelate tool (I can't get deepTools installed on my server). But I can't find any litterature on it and how it calculates the correlation. I don't know anyone coding in C here, so I can't really understand the code and don't really have time to dig in it.

So: How does UCSC bigWigCorrelate works? Is it Pearson correlation? How does it bin the data?

I'd be happy if I can get some information from here!

Thanks,
JS