plotFingerprint -b $chip --JSDsample $input

[thomasmanke]

The subject line will not calculate JSD, Chance etc. Instead one needs to specify

plotFingerprint -b $chip $input --JSDsample $input

This is somewhat counter-intuitive. Would it make sense to add the JSDsample automatically to the list of bam files?

[dpryan79]

I can have it added in if it's not already there I suppose. The reason for the current implementation is simply that plotFingerprint pre-existed the JSD code, so that was the simplest implementation.

[dpryan79]

This is implemented in develop. Please give it a test with module load deeptools/develop.