James Ferguson

Perhaps if you make a benchmarking protocol, people can run it and post the results. I'd be happy to run it on all of our machines. James

I have added more error handling for this in the `errors` branch

Hey, Can you help me understand the advantage of having blue-crab in the biocontainer registry? what problem does this solve vs installing with pip? I don't know much about the...

I would like to avoid conda if I can, due to the weird business practices they have engaged in recently. I am confused why nf-core doesn't accept pypi packages, or...

Okay you've convinced me. I'll make a conda recipe 😅 James

Hey, If you converted the blow5 files to pod5 using the `blue-crab` converter, then ran with dorado-server or dorado, you would find you get a similar result. This looks to...

Hello, That looks like you are putting a gzipped signal file to SquigglePlot. It currently doesn't accept gzipped signal files. Try unzipping it and trying again. James

Hello, You are missing the argument in front of the signal file in your command. It should be ``` python /cm/shared/apps/squigglekit/1.5.1a/SquigglePlot.py -s /condo/kisslab/tmhtxt53/GridIon/m6Apaper_data/SquiggleKit/SRR8767348_squiggle-pull.tsv --raw_signal --save SRR8767348_squigglePlot.png --save_path /condo/kisslab/tmhtxt53/GridIon/m6Apaper_data/SquiggleKit ``` James

Hello, SquiggleKit does not do base-to-signal alignment or modification detection. It was built primarily to allow users to visualise the signal data to get more comfortable with the data to...

Hey, I'm not from ONT but this might be the tool you are looking for https://github.com/hiruna72/squigualiser Cheers, James