Closed Ge0rges closed 11 months ago
Turns out the bedmethyl file was not consistent in its use of tab as a delimiter. See this issue, if using bedmethyl files generated by modkit.
Hi @Ge0rges
Thanks for raising this issue, I think this will become more relevant in the future.
I will have a closer look into the problem, probably we should add support for "modKitBedmethyl" format.
Best, Alex
I believe the modkit team is switching to the standard tab delimited file see https://github.com/nanoporetech/modkit/issues/43#issuecomment-1734502646
Hello,
I was wondering what the correct way to read in a bedmethyl file with all context 5mC and 5hmC methylation is? I tried:
methObj=methRead(files.list, sample.id = list("methylRawList"), assembly="106_sub", treatment=c(0), context ="CHH", pipeline=list(fraction = FALSE, chr.col = 1, start.col = 2, end.col = 3, coverage.col = 10, strand.col = 6, freqC.col = 11))
My bedmethyl file is standard and looks like this according to this standard.
However I get the following error:
where files.list points to a string of an absolute path to bedmethyl file.