Assistance Needed: Generating the model.gtf File

[dawangran]

Hello,
I'm currently facing an issue with generating the model.gtf file, which is essential for my analysis. Could someone provide guidance on the correct approach to create this file?
Thank you for your help.
Best regards,
Dawn

[andrewprzh]

Dear @dawangran

Could you elaborate what is your input and what problems exactly are you facing?

Best
Andrey

[dawangran]

Hello,
I am using sqanti3 for transcript isoform identification, which requires a model.gtf file. I understand that isoquant can generate a model.gtf file, but I am unable to locate this file in the output of spl_isoquant.

Best regards,
Dawn

[andrewprzh]

Dear @dawangran

Spl-IsoQuant is designed for reference-based analysis of single-cell and spatial data, and currently does not construct novel transcript models.
I suggest using standard IsoQuant for this and provide your data as bulk.

Best
Andrey

[andrewprzh]

Dear @dawangran

We released a new Spl-IsoQuant 2.1, which is capable of detecting novel isoforms as well.

Best
Andrey