Yupeng He

It is possible by running DMR finding twice on allc files with just + strand CpGs and a separate set with just - strand CpGs. The reason for DMRfinding combing...

> If I want to calculate the DNA methylation level in the promotor region of + stand genes using methylpy add-methylation-level, do I need to think about +/- strand? In...

That should be fine. Methylpy works for human genome which is larger than 512Mb. Is the error reproducible? If so, having some files to reproduce the error will help me...

Cool. Do you need any help with this? Downgrading cutadapt to the version methylpy supported is one option. Alternatively, we can run cutadapt manually and then run methylpy with trimming...

Hey unfortunately methylpy cannot correctly handle data from non-directional library.

Thanks for the suggestion. Unfortunately, this feature is not currently supported by methylpy yet and it is not trivial to implement. I cannot promise that this feature will be available...

Maybe it is the index file. Can you check whether the chromosome information is correctly stored in `.idx` files? For example, `guo_1.tsv.idx` and `hua_1.tsv.idx`.

Yes, DMRfind only needs allc files. Do you mind to share the two files for me to reproduce the error?

Can you reproduce the error with the first say 30 lines of allc files?

It is totally fine to set the last column to be 1. The current issue is that the context column (4th) format in the input file is not supported by...