Alternative first exon undetected

[IsabelGam]

Hello,

I recently started to use ASpli to quantify the alternative splicing levels of my gene. My gene has 3 isoforms which only differ from each other by one exon.

• The first one has all exons.
• The second one has an exon spliced.
• The third one is like the first one, but with a different starting exon, which does not overlap with the starting exon from the two other isoforms.

The function binGenome() can detect the exon skipping from the second form. However, it does not detect the splicing event generated by an alternative exon 1. For now, I modified the GTF file to allow an overlap of the alternative starting exon, so that binGenome() detects it as an alt5'ss event. I wonder if there is a solution to this problem since I want to quantify alternative splicing levels for other genes, which also have an alternative starting exon (or ending exon).

Thanks

[jcgrenier]

Hello! @estepi, any idea about this issue? Thanks a lot!

[estepi]

Hi both!

We can ignore/include "terminal" exons in our script. I need some info from your side:

• How did you run the function? (including which version of ASpli are you using)
• Which output do you see in BinGenome Log file? Can you check if the exon you are interested is labelled as "Terminal".

thanks a lot for using ASpli, looking forward for your info

pd: can you copy-paste the issue in this repo please: https://github.com/chernolab/ASpli/issues