Correlation between Chip-seq BAMs
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 :)
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Devon Ryan
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anu014
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anu014
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They're both useful and often it's best to look at both, but if I had to choose one I'd choose spearman.
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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.