Jared Simpson
Jared Simpson
@NickyPan what does your `make` command look like, and can you give the full output from it? I suggest letting nanopolish clone and install the built-in htslib.
Hi Laura, The chromosome positions should not vary, can you give an example of the problem? Jared
Maybe I misunderstood, are you using two difference reference genomes?
In this screenshot the sites are fairly low coverage (only a few reads covers each site) so it is hard to say whether it is biological variability or just sampling...
Hi Laura, Unfortunately I don't have a strong recommendation here, as our focus is on the detection of methylation rather than downstream analysis. We've played around a little with [DSS](https://bioconductor.org/packages/release/bioc/html/DSS.html)...
>After that, I used "cat" command to merge all FASTQ files into one FASTQ and then I used Nanopolish Index. Should I use it before concatenation of FASTQ or it...
That is very strange and I can't immediately think of a reason why this would happen. What is the sequence in `transcript_oligo.fasta`?
IIRC nanopolish will tolerate Us in the basecalled reads but it may not tolerate Us in the reference sequence. Try converting the reference and see if it works.
Thanks for tracking that down, I may fix this (or give a better error message) in the future.
We do have an `r10` branch here on github but it is very old as you've seen so I doubt it is worth running. Training an R10.3 model is on...