Should I turn on or turn off the "--u_substitution" for guppy basecalling if I use Flair for my downstream analysis?

BrooksLabUCSC / flair

Full-Length Alternative Isoform analysis of RNA

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Should I turn on or turn off the "--u_substitution" for guppy basecalling if I use Flair for my downstream analysis? #228

Closed yjx1217 closed 1 year ago

yjx1217 commented 1 year ago

Dear developers,

Should I turn on or turn off the "--u_substitution" option for guppy basecalling if I use Flair for my downstream analysis? Not sure how Flair treat U in the transcript sequences. At least in Flair's plot_isoform_usage script, I saw 'U' is not defined in variables such as base_colors and reverse_complement. Thanks in advance!

Best, Jia-Xing

Jeltje commented 1 year ago

Flair runs minimap2, which I believe does not expect U bases, so it's best to turn them into Ts.