Question: Correlation between Chip-seq BAMs
0
gravatar for anu014
3.1 years ago by
anu014180
India
anu014180 wrote:

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 :)

correlation next-gen chip-seq • 938 views
ADD COMMENTlink modified 3.1 years ago by Devon Ryan97k • written 3.1 years ago by anu014180
2

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 REPLYlink modified 3.1 years ago • written 3.1 years ago by venu6.7k
1
gravatar for Devon Ryan
3.1 years ago by
Devon Ryan97k
Freiburg, Germany
Devon Ryan97k wrote:

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 COMMENTlink written 3.1 years ago by Devon Ryan97k
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