deeptools computeGCbias: what are the columns in the GCbiasFrequenciesFile?

Question

[tanagholattorobche]

Hello,

There are 3 columns in the GCbiasFrequenciesFile that deeptool's computeGCbias function outputs. What are these columns?

0.000000000000000000e+00 3.100000000000000000e+03 1.000000000000000000e+00 1.000000000000000000e+00 2.258000000000000000e+03 2.478874781436007091e-01 2.000000000000000000e+00 3.229000000000000000e+03 3.466893314637661261e-01

source code shows these 3 names but it's unclear what they exactly represent.

F_gc = data[:, 0]

N_gc = data[:, 1]

R_gc = data[:, 2]

Thanks! -m

Answer 1

[Devon Ryan]

This is meant for internal use only and that tool is deprecated, so there's no documentation for it. From my understanding of the code (I've only ever made it work in python 3) the meanings are:

• N_gc: The number of reads with a given GC content
• F_gc: The number of reads spanning regions with a given GC content
• R_gc: The scaled ratio between the above values

The number of rows should be equal to 1 plus the estimated median fragment length. I've honestly never looked into this code much, it was deprecated already when I took over deepTools in 2015.