Entering edit mode
8 weeks ago
Thank you for your reply! I tried with modkit in conda environment and I do not know why always have error , is not because of my code or ? I want to get mCpG and 6mA from my mapped bam file .
@GenoMax wrote:
Comment: how extract CpG methylatiuon calls from nanopore long sequencing bam file ?: Do you know if your file already has the methylation calls? If they are there then you can use modkit ([LINK][1]). Otherwise you will have to go back and re-basecall methylated bases with dorado and pod5 files from original data folder. [1]: https://github.com/nanoporetech/modkit
Please do not repost problems with a solution in separate threads. If you are having an issue continue in the same thread using the
ADD COMMENTbutton.You don't provide any specifics on what the issue is. Which conda env are you referring to? Are you using the compiled binary provided here: https://github.com/nanoporetech/modkit/releases
We should move this discussion back to the original thread: how extract CpG methylatiuon calls from nanopore long sequencing bam file ? .