Apply FLARE on long read sequencing (ONT)

[EmelineLG60]

Hello everyone,

First of all, thank for reading me. I am a phd student in biology, and I am learning on my side some bio-informatics stuff, without any background.

Since several months, I have hard time running correctly? FLARE on my data.

For context, we have done long read sequencing (Poly(A) enrichment, PromethION, R10 and guppy aligment) on two different samples : APOBEC1 alone and APOBEC1-RPS2 (like Brannan did in his paper in 2021 : Ribostamp). I want to highlight specific isoformes associated to ribosomes.

After running Flare protocol (no trouble for that, the readme file is pretty clear, thank to you), and doing metaplot, I see more editions in transcripts in my APOBEC1-RPS2 condition versus APOBEC1 alone. But, the different isn't really neat. I have lot of edition in the end off 3'UTR too.

After reading all the scripts python, I have found several parameters. I have played with some off them, but the result isn't neat too.

Did someone test that with recent R10 with ONT technology ? And what was your parameters for that ?

Thank you a lot for your help and advice,

Emeline