4 votes
Accepted

Nanopore Flongle vs MinION

For us, R10.4.1 Flongle flow cells are running at reduced yield due to lower numbers of working pores (something like 10-20 pores instead of 30-60 pores for R9.4.1 flow cells). This doesn't really ...
gringer's user avatar
  • 13.9k
3 votes

Is my reference sequence too small?

That's not the right way to do it. You either have reference or not. If not, you need to assemble one (that problem is called genome assembly). If yes, you map all the reads to the whole reference - ...
Kamil S Jaron's user avatar
3 votes
Accepted

Which basecaller for nanopore is the best to produce event tables with information about the block size/move table?

ONT's newest basecaller, Dorado, can do this for SAM output with the --emit-moves argument. It was added in this commit. Dorado can be downloaded from here: https://...
gringer's user avatar
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1 vote
Accepted

single_to_multi_fast5 does not collect all the single files if the input folder contains mixed types of fast5 files

It looks like you're creating too much additional work for yourself. What I'm trying to lead to with my comments is that the file names should help in working out if a file represents single reads or ...
gringer's user avatar
  • 13.9k
1 vote

How should I use dorado basecaller to calculate translocation time? Can I change models' config files?

In pod5 files the number of samples prior to the adapter/sequence should be encoded in the metadata, and can be looked at using ONT's pod5 inspect tool: ...
gringer's user avatar
  • 13.9k

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