This is a test version of Biostars. For the public version, visit https://www.biostars.org.
deeptools computeGCbias: what are the columns in the GCbiasFrequenciesFile?

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

correctgcbias computegcbias gcbias deeptools
• 1,298 views • link
updated by GenoMax GenoMax • written by tanagholattorobche • tanagholattorobche

1 answer

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.

• 0 views • link
written by Devon Ryan Devon Ryan

Log in to answer this question.

More posts like this