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skovaka / uncalled4

MIT License
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beginners question #16

Open mocherry opened 6 months ago

mocherry commented 6 months ago

Dear Sam,

I am sorry for asking what may sound a trivial question, but I am quite new to this business: what would be the complete, correct command line for:

uncalled4 align ...

if I wanted to use it for a sam file produced with: dorado basecaller rna004_130bps_sup@v3.0.1 PATH TO FAST5-files --modified-bases m6A_DRACH --emit-moves --emit-sam > uncalledtest.sam

to do the analysis with data from RNA004 sequencing???

Thanks alot in advance for your help and consideration. Best, Matthias

skovaka commented 6 months ago

That command looks good, but unfortunately we currently only officially support RNA002 and RNA001. I'm working on RNA004 alignment, and you can find a preliminary implementation on the "dev" branch. The exact parameters for the preset might change after I test with modification detection, but if those results look good then it could be the final version. I can hopefully finalize it in the next week or two and will then merge with the main branch.