How to estimate PSI of a new input sample on pre-called events

[sckinta]

• spladder version: 3.0.3
• Python version: 3.9.13
• Operating System: rhel7.9

Description

We have previously run spladder on a cohort using the recommended documentation, and built a prediction model using the PSI output from spladder event calls for the downstream analysis. Now we have some new RNA-seq samples (bam files), and want to map the new bam files to the previous called events, and generate PSI for the new samples so that we can use that prediction model. Can this task be done by spladder build?

In the documentation, there is an option spladder build ... -use-anno-support .... Is this the option i am looking for? Could you please elaborate how to use this option in above task?

Thank you

[akahles]

Dear @sckinta,

Thank you very much for reaching out and for using SplAdder. The re-quantification of existing events on new input files is currently not supported by SplAdder. I understand the use case and will add it to the ToDo list. That said, we are maintaining the tool on a best-effort base, so I cannot promise a specific time until when the feature is implemented. I will keep the issue open to keep track.

Cheers,

Andre