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gagneurlab / drop

Pipeline to find aberrant events in RNA-Seq data, useful for diagnosis of rare disorders
MIT License
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Aberrant splicing theta (θ) values width all have the same value #517

Closed carlalbc closed 4 months ago

carlalbc commented 4 months ago

Dear DROP team,

I am writing an issue because I am unsure if I have an error in my data, or my configuration files.

When I evaluate the results obtained after running the aberrantSplicing module of DROP (FRASER) I find that all the hits for the splicing type theta have a width length of only 2nt. I have run the same pipeline with three different datasets and it seems to be a recurrent issue for this value.

Do you have any idea why this could be? Could it be that I have a configuration problem? or that I have a parameter set or unset wrongly in FRASER?

Table for reference:

image

Thank you in advance for your help!

vyepez88 commented 4 months ago

Hi Carla, thanks for using DROP. Actually, that is not an error. The metric theta tests splice sites, not junctions, so the width is always 2 (see the start and end columns).

carlalbc commented 4 months ago

Ah, I see, perfect then. I was a bit confused! Thank you :))