Classification of adjacent genes in In the same direction by collapse_isoforms_by_sam.py about cdna_cupcake

[Magdoll]

Hi @Trandamere ,

As you have observed, this point, collapse script is very generous with grouping genes --- any transcripts that overlap by 1 bp on the same strand are grouped together as a "locus".

I don't have plans to introduce more nuanced gene-clustering at this point, unfortunately.

If you have a reference genome with existing annotation, you can compare the results against SQANTI to help further tease the genes apart.

Ultimately, the goal of the collapse script is to identify transcribed loci, not to identify genes per se. That requires expertise and manual curation.

--Liz

[Trandamere]

Thank you！