BAM/SAM input option

[carolinamonzo]

Discussed in #273

^{Originally posted by apollo994 March 21, 2024}
Hello SQANTI team,

I've started using SQANTI3 to directly evaluate reads instead of gene models. This is a really helpful feature when comparing two sequencing runs/technologies and you want to avoid the bias from the transcript model construction algorithm. In this context, it would be helpful to have an option to input an alignment file directly. This would skip the time/resource consuming step that, in many cases, has already been done in previous steps.

Thanks a lot for sharing and maintaining this project!

[carolinamonzo]

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.