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estepi / ASpli

Analysis of alternative splicing using RNAseq
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Splicing event assignation #4

Open bellenger-l opened 5 years ago

bellenger-l commented 5 years ago

Hi,

I was wondering what the event "-" corresponds to ? It is not described in your manual in Bioconductor. The major feature event of my data are labelled as "-" and I was curious to know why.

Thanks, Lea

estepi commented 5 years ago

Hi Lea, When the minimum local gene model contains two isoforms bins are labelled. In case this region (bin) doesn't contain alternative isoforms, we use "-". We say all they are "putative alternative bins" because you can find some of them being spliced different accross conditions Thanks for your comment, we will clarify next version of the manual.

bellenger-l commented 5 years ago

Thanks for your quick response !

I was suspecting that because of your first paragraph in 3.1.1 but I wanted confirmation. Also, I am not sure to understand correctly the term of "minimum local gene models"...

A last question, how do you proceed for exon/feature bin that are shared by different gene ID ? I can tell with the DEXseq tool because this is written "GeneID1+GeneID2:E001" for example but it is not the case with ASpli, do you discard them ?

estepi commented 5 years ago

We discard genes that full overlap another gene-> those whose coordinates are exactly the same Then, we report in the column "locus overlap" if oter genes overlap this regio. Bins names are defined using an arbitrary order. The only thing you can check is the column "locus overlap" just to be aware that this bin could be conflictive.

qicaibiology commented 5 years ago

Hi: I found that for a certain event, intron retention, for example, the event number under file intron.irPIR is different with junction.PIR. Why this is happening and how should I treat them?