Eduardo Eyras

Yes, no problem I reckon that to link the info you'll need to add a column to the .ioe / .ioi file I'd say it is better to add it...

Sorry, I do not understand your question Also, the coordinates e.g. 2533201 and 2532751 should be in the GTF as alternative 5' splice sites (the exonic position). Do you mean...

Could you specify whether it is the coordinates of the alternative sites, or just the GTF of the events? I cannot tell from the IGV pictures what the exon positions...

Thanks, so the coordinates in the event do not appear in the GTF at all? I'm wondering where those two positions in the A5 event come from in the GTF....

Thanks for your message plotting the input values could help understand what is happening. E.g. you could plot the deltaPSIs as a function of average TPM, as described in the...

Thanks for your message. What you describe sounds like a possible formatting error in the input files. Could you please check that the headers are defined as described in the...

Hi, you can use a GTF generated by yourself with e.g. StringTie or any other method. The important thing is that the GTF contains transcripts and genes, and that you...

Dear Xi Xu, Thanks a lot for your email. If you have two groups, SUPPA provides a function to calculate the differential splicing between the two groups. It looks at...

Thanks for the questions and inputs We’ll add some info in the README to help with possible issues with the input Keeping polyA’s should be actually better for clustering and...

Hi Tasy, Thanks for your email. Perhaps the transcript IDs in your GTF and in your expression file are different? They look different in your screen captures. SUPPA would not...