PSI-Sigma filtering error: "can't find wings in the database"

[asethi-1]

I am trying to do alternative splicing analysis on some drosophila RNA-seq.

During filtering, PSI-Sigma is throwing an error:

===PSI analysis spent 0.0033 hours.=== Filtering ΔPSI results... Filtering mode = 0 Reading... ./PSI-Sigma_reference.gtf.mapping.txt Reading... PSIsigma.db (ERROR) CR44968, CYLD can't find wings in the database. Aborting... ===Filtering spent 0.0003 hours.===

Any idea what is causing this?

[asethi-1]

Unrelated follow up question: In the output of PSI-Sigma, event types can be "S" or "W". What do these stand for?

[wososa]

Hi @asethi-1 ,

Thanks for trying PSI-Sigma. The error looks like that the gtf format is not supported. Could you either download the gtf file from Ensemble or give me a link so that I can see which format error it is?

Thanks, Woody

[asethi-1]

The issue still persists, but looks a little different:

===PSI analysis spent 0.0011 hours.=== Filtering ΔPSI results... Filtering mode = 0 Reading... ./PSI-Sigma_reference.gtf.mapping.txt Reading... PSIsigma.db (ERROR) CR45778, dUTPase can't find wings in the database. Aborting... ===Filtering spent 0.0003 hours.===

I use the drosphila genome annotation from Ensembl.

By the way, I have noticed that in the output of PSI-Sigma, event types can be "S" or "W". What do these stand for?

[wososa]

Hi @asethi-1 ,

Sorry for the delay. It looks like that your .gtf file may not be in the compatible format. I have used PSI-Sigma for primate and non-primate species, but I haven't had chance to do Drosophila. I am not sure if the Ensembl's Drosophila .gtf file is different from other species. Based on your log, it seems like that the format of .gtf file name isn't the format of Ensembl's .gtf file. Did you modify the .gtf file?

Thanks, Woody