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
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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-PicardThanks. I'm looking into using picard.