Open carolinamonzo opened 6 months ago
Hi @apollo994! We agree, it's something that we have in mind but haven't had the time to implement it yet. However, you can give a GFF to SQANTI instead of starting from scratch and having to construct transcript models.
What you can do is use the spliced_bam2gff tool from Nanopore to transform your bam to GFF (careful with the -t option, it is a reported issue in the tool's repository that instead of corresponding to threads, it's a threshold of to classify all deletions larger than the value as introns). And then run SQANTI on the GFF of your reads.
Discussed in https://github.com/ConesaLab/SQANTI3/discussions/273