Correlation between Chip-seq BAMs

Question

[anu014]

Hello Biostars!

Which Correlation coefficient would you prefer to get correlation between BAMs - spearman or pearson? I need to input this in deepTools's plotCorrelation program. My data is Chip-seq data.

Thanks in advance :)

[venu]

I would try both and see the difference. If the BAM are of completely difference conditions (i.e normal - cancer), both should work fine. If the all BAM files related to same condition, I observed "spearman" working better.

Answer 1

[Devon Ryan]

They're both useful and often it's best to look at both, but if I had to choose one I'd choose spearman.