Jared Simpson comments

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                                            Jared Simpson

Very high methylation frequencies from PromethION wgs run

Maybe try comparing two of your blood samples against each other?

Please port to Python3

Hi @tillea, If possible could you point me to the problematic python2 scripts? Jared

Please port to Python3

Thanks, that is helpful. I will incorporate these changes. Jared

Please port to Python3

Hi @tillea, @paultsw has just pushed the 2to3 changes. Could you take a look? These changes will be incorporated into the next tagged version. Jared

Please port to Python3

@tillea I've now tagged a version with these changes as `0.11.2` - sorry for the delay. Let me know how it looks.

HI @yamkela-mg, I don't recommend nanopolish for polishing genome assemblies anymore, medaka gives consistently better results. If you wish to continue your nanopolish run I would suggest checking which .vcf...

call methylation_segmentation fault

It appears the GM12878 files are one-read-per-fast5 (the old format), rather than multi-fast5. As a test could you try to re-pack the fast5s using [single_to_multi](https://github.com/nanoporetech/ont_fast5_api#multi_to_single_fast5) to see if it resolves...

Allow multiple fastq files from the same sample to be used in a single nanopolish run

Note you can now (since late last week) give the `-d` argument to `index` multiple times to avoid moving fast5s around (or creating symlinks) but you still need to make...

nanopolish error too many argument

Hi, Were you able to solve this? I don't see an obvious error, but you've provided the .bai file instead of the .bam file for the `-b` argument. Jared