Jared Simpson
Jared Simpson
Hm, if it worked on barcode01 and barcode 03 it might mean the fast5 for barcode02 is corrupted somehow. Perhaps try to identify which fast5 doesn't work?
I don't think it is worth it, I would try medaka instead. Jared
Sorry about this, the openssl package in rust seems like a common source of problems. I do intend to provide pre-compiled binaries - I'll put it back on my todo...
Hi @ccbruels, Could you try this binary? https://github.com/jts/smrest/releases/download/0.1.0/smrest-0.1.0
I just tried a clean install and it worked. Please provide some details (OS, build error log).
That's not an HDF5 error. See here: https://github.com/jts/nanopolish/issues/125
both the header files (`zlib.h`) and the compiled libraries are needed to compile htslib/nanopolish. I don't use WSL2 so it is hard to say why they can't be found. On...
Yes, there is internal trimming. The signal-to-read alignment step can discard the ends of the read, and also the methylation calling algorithm avoids calling at the ends of the signal...
Nanopolish skips regions that have long regions of high CpG density as it is computationally too expensive to call this - is this possible for this case?
Hm, it might be this check then: https://github.com/jts/nanopolish/blob/21c75db77b0e1338989be2d5c6bc96eca7c86c37/src/basemods/nanopolish_basemods.cpp#L354 You could try commenting it out to see if the call at 307 appears.