Deeptools: Custom gcbias plots in R possible?

Question

[RJDan]

Hello I am new to deeptools. I am using the computegcbias tool for a collection of bam files (split by chr, individual and 3 different sequencing methods). I ran the function thinking the output of the --GCbiasFrequenciesFile would allow me to import the results into R and then create some summary stats.

I could not find a description of what is exactly in these files. My output has three columns and 186 rows but it is not easy to figure out what they stand for. I found this question : deeptools computeGCbias: what are the columns in the GCbiasFrequenciesFile? but it is 5 years old now so maybe something has changed.

Is it possible to export the results from deeptools to be imported into R for custom plots?

RJDan

[GenoMax]

Devon Ryan is one of the author's of deepTools. His answer in the thread you linked should still be valid. He also warned that the tool was deprecated in ~ 2015 so you should perhaps look for an alternate option.

You could instead use picard: https://gatk.broadinstitute.org/hc/en-us/articles/360037593931-CollectGcBiasMetrics-Picard

[RJDan]

Thanks. I'm looking into using picard.