Removal of single Isoform genes prior to diffsplice analysis

[JamalEH]

Dear Team,

I was wandering if we could remove the single isoform genes prior to runing differential AS analysis, since only multi-isoforms genes are subjected to AS changes. Would this affect the statistical significance (-gc option output) as well as the PSI values for each event?

Thank you so much in advance!

Best regards, Jamal.

[EduEyras]

Hi Jamal,

thanks for your question. Single isoform genes are not included in the analysis, since only the transcripts that participate in the AS events are used. I cc JC, who implemented the method, in case he wants to add anything

cheers

Eduardo

On Fri, 11 Oct 2019 at 22:30, JamalEH [email protected] wrote:

Dear Team,

I was wandering if we could remove the single isoform genes prior to runing differential AS analysis, since only multi-isoforms genes are subjected to AS changes. Would this affect the statistical significance (-gc option output) as well as the PSI values for each event?

Thank you so much in advance!

Best regards, Jamal.

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[JamalEH]

Dear Eduardo, Thank you so much for your reply!

So even if the single genes are present within the GTF file there is no AS event will be assigned to them (since they have only 1 isoform). I was just afraid that there might be an exon overlapping between two different isoforms from totally different genes (one single isoform gene, with another multi-isoform gene) and that would affect PSI calculation. I read a bit more and found that SUPPA uses an isoform-centric approach so I shouldn't be worried about that.

PS: would you advice me to use the median dPSI if having only 3 replicates per condition? or is better to use the mean since I have only limited number of replicates per condition? I got more significant events when using the median instead of the mean dPSI, and both overlapped up to 60% of events. Can I use the union of the two?

Thank you so much again, dear Eduardo! Best regards, Jamal.