fanc compare with juicer inputs does not seem to scale the matrix

[varunkas]

Hi,

Thanks for developing this tool. :)

I have been trying to get the fanc compare to work on juicer files, but it seems like despite not adding the -S tag, the comparisons (both fold-change and difference) are dependent on the total number of valid pairs. The output does show that it is calculating the scaling factor, but it does not seem to be taken into consideration? For example:

juicerA has 400 millon read pairs
juicerB has 300 millon read pairs
juicerC has 300 million read pairs

juicerA-juicerB results in a matrix with overwhelmingly +ve values. Whereas juicerC-juicerB does not. I thought that scaling the matrix for the total number of read pairs will take care of it?

Is this the intended behaviour? Am I missing something?

Thanks,
Varun