Jared Simpson
Jared Simpson
Sorry about this, its been a long standing issue with direct RNA data. Will try to address it when I have a chance.
Hi, "c" means the contig is circular. If this is a plasmid or other extrachromosomal element it might have very high depth, which will take nanopolish a long time to...
Thanks @jmarshall, I missed that when reviewing the original discussion before posting this issue. I agree using `N` works around this issue. Is the mapper allowed to modify/fix `MM` tag...
I've been mulling this over for a few days and leaning towards adding another flag. Without a flag the counts can be relative to the original (possibly unknown) sequence, and...
Hi, Can you show me the command you ran, and the VCF file that nanopolish output? Thanks, jared
Ah, I just noticed now that it is the 13th base of the genome. It likely is missed because it is how close to the start of the chromosome it...
Which shell are you using? It looks like it didn't like substituting in the hdf5 version: ``` wget https://support.hdfgroup.org/ftp/HDF5/releases/hdf5-${version_major_minor}/hdf5-1.13.0/src/hdf5-1.13.0.tar.gz; ```
Hm, it appears some files are missing from the hdf5 FTP. Can you run: `make HDF5_VERSION=1.13.2`?
Ah sorry, I forgot to mention that `clang` is not supported. You'll have to install gcc then compile with `make CC=gcc CXX=g++` (setting `gcc` and `g++` as appropriate, on my...
That's a new one to me as it appears the code compiled successfully but it crashed the linker. A bit of googling hints that it might be a homebrew problem....