Kieran O'Neill

I don't think we've had any issues with nanopolish and recent versions of guppy. The hdf5 format which fast5 is a subset of hasn't changed, and your failures are in...

Nanopolish methylation calling has pretty consistently out-performed the fancier deep learning methods for a while now. That's been both in our hands and in the hands of other groups who've...

Thanks @jts ! mbtools look very useful for getting the data out of the bam, and I guess we'll just have to wait for the methylation_bam branch to be done...

Thanks @marcus1487 Would it be possible to get a version of the `mod_basecalls` BAM file that has been mapped? Ultimately what we want is to have a single BAM containing...

Yep I'm having the same issue -- SALSA always runs 5 iterations (well, maybe 4 -- it looks like "iteration 1" is just the baseline assembly). This is different from...

Thanks for the explanation @skoren ! It might be good to update the documentation/remove the parameter. And is there any way to fine-tune when it stops? I have an assembly...

I mean, the answer from the Juicebox team seems to be "Don't use SALSA if you want to edit your assembly in Juicebox". Or alternately to run the final assembly...

Juicebox itself can open the .hic file and visualize it, but the parts of Juicebox for editing the assembly (aka "Juicebox assembly tools" or JBAT) require an "assembly" .hic file,...

I am having the same issue. Shift-click also doesn't do what's shown in the tutorial video -- it just opens up a view of the scaffold rather than selecting it....

@sa501428 is there example data somewhere to test whether this is working at all? The .assembly file I'm using was generated from the SALSA .agp file, using a script from...