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landau-lab / ONT-sc-splice

Tools for detecting alternative splicing events and genotype in single-cell gene expression data.
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Question about exon skipping annotation #4

Open apsteinberg opened 6 months ago

apsteinberg commented 6 months ago

Hi there,

Thanks for the wonderful new tools! I have a question about the output of the script new_annotator_with_skipping.py

In the README.md it says that "Events will also be classified as exon skipping events or alternative splicing events.". I see in the example output here that cryptic 3' and 5' splice sites are annotated in the "verdict" column. But I don't see annotations for exon skipping events. Can these be determined from the two final columns, "relStartExon_skipping" and "relEndExon_skipping"?

Thanks for your time and help.

Best, Asher

mcortes-lopez commented 5 months ago

Hi Asher,

Sorry for the late reply, I did not see this on my email. Yes, that was an initial issue. We implemented a bit more recently a fix in this script. It takes the output file of the pipeline and considers the information of the 5' and 3' verdicts to annotate the exon skipping events. I will try to update the documentation for the more recent Snakemake implementation of the different steps of this pipeline in the next couple of months, but feel free to take a look to that as well.