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timbitz / Whippet.jl

Lightweight and Fast; RNA-seq quantification at the event-level
MIT License
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PSI = 0.99 when no reads on event #42

Closed mirimia closed 7 years ago

mirimia commented 7 years ago

Hi Tim,

I'm starting to look at real outputs. I was curious about the following:

ENSMUSG00000111339 2 chr7:102236094-102236346 + CE 0.99 NA NA NA NA NA NA NA

Do you assign psi=0.99 when there are no reads aligning? I saw this in all cases I looked. If so: why?

Thanks Manu

timbitz commented 7 years ago

Good point, that string of NAs is not sufficient information given the current output format. (I started that early on, before most of those PSI trailing columns existed etc. So PSI=0.99 or PSI=0.0 was assigned for constitutive inclusion or exclusion, always where the total_count > 0. In the case where there are no reads aligning PSI=NA always.

I have changed this in #43. Now for constitutive inclusion or exclusion, the rest of the columns are filled in (and 0.99 has been substituted for 1.0 as it should have been). The output for a constitutive inclusion column now looks like this:

ENSG00000118873.15_2 2  chr1:220406141-220406205   -  CE 1.0   0.202 0.794,0.996 12.0  K0 0.0   1-2-3:1.0   NA

and constitutive exclusion:

ENSG00000116191.17_2 15 chr1:178861365-178861442   +  CE 0.0   0.5143   0.0127,0.527   3.0   K0 0.0   NA 14-16:1.0
timbitz commented 7 years ago

Closed by #43