I'm trying to plot the coverage of a bam file from a ChIP-seq experiment via NGSplot and I get the following error:
Configuring variables...Error in CheckRegionAllowed(reg2plot, default.tbl) : Unknown region specified. Must be one of: bed Execution halted
This is the command I'm using:
ngs.plot.r -G mm10 -R tss -C myfile.bam -O mybamfile.ngs
If I change the -R from "tss" to "bed" and specify a bed file I get from the PeakCaller software, it works just fine. However, I want it to take into consideration only the bam file
Any ideas why I'm getting this error message?