Jared Simpson

Can you send me the read ID? I have that data here

This read works for me, when I download it using `wget http://s3.amazonaws.com/nanopore-human-wgs/rel4-nanopore-wgs-4249180049-FAF09701.fastq.gz`. I'm using: ``` samtools 1.10 Using htslib 1.10.2 Copyright (C) 2019 Genome Research Ltd. ``` ``` minimap2 2.17-r941...

Could you provide the fastq and bam file containing this single read? You should be able to attach it here, or email to [email protected].

Thanks, I'm on vacation now but will try with your data when I return to work. Could you try the [methylation_bam branch](https://github.com/jts/nanopolish/tree/methylation_bam), which uses a more recent htslib, to rule...

I'm glad to hear that, thanks for reporting back so quickly. I'll try to merge in the htslib upgrade soon.

Hi, Sorry for the slow response. We typically aim for 30-50x coverage but it is very much dependent on what you want to do with the data. Jared

Thanks for letting us know the problems you had. @jopineda is currently revising the tutorial - Joanna can you make sure these comments are addressed?

Hi @marynias, I'm afraid this is pushing the limits of what is possible with nanopolish. The error is caused by the genotyping step, which will examine all possible configurations of...

Great. The core issue is that the nanopore measures the signal from multiple overlapping bases, so we need to consider clusters of variants collectively rather than one-by-one. Nanopolish is conservative...

Hi, If you upgraded nanopolish from 0.7.x to 0.8.y then you need to run this preprocessing step: ``` nanopolish index nanopolish_barcode11_emily.fasta ``` Afterwards, the first command you ran should work....