Entering edit mode
14 months ago
nach.mcnach
▴
10
Working with ChIP-Seq data, I am looking into the various normalisation options available on bamCompare (version 3.5.0) to produce a bedgraph of log2(chip/input) values.
RPGC is given as an option in the documentation, however I get the following error:
RPGC normalization (--normalizeUsing RPGC) is not supported with bamCompare!
So that is it, it appears. I thought it was an error in the documentation as bamCompare shares a lot of optiopns with bamCoverage. However I've seen other people here mentioning using RPGC with bamCompare on ChIP and ATAC-Seq data.
Is it possible to implement RPGC at all with bamCompare?
