Question

Correlation between Chip-seq BAMs

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6.5 years ago

anu014 ▴ 190

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 :)

ChIP-Seq next-gen correlation • 1.5k views

ADD COMMENT • link updated 6.5 years ago by Devon Ryan 104k • written 6.5 years ago by anu014 ▴ 190

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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.

ADD REPLY • link 6.5 years ago by venu 7.1k

score 1 · Answer 1 · 2017-10-19

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6.5 years ago

Devon Ryan 104k

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

ADD COMMENT • link 6.5 years ago by Devon Ryan 104k