Eduardo Eyras

Hi, Do you get this error for all transcripts or just a few? The ioe will include all events and related transcripts from the annotation, but some transcripts may not...

Other possibilities are: * file formats are not correct (e.g. no tab present, wrong number of labels, hidden characters... ) * transcripts have zero expression (or no entry) in the...

Hi, this expected by the definition of the RI event In the default mode, the RI is quite restrictive and it expects that the exon retaining the intron also share...

You can run it only for RI events, which may be probably the case where you want to relax the constraints For all other event types, you can keep the...

Apologies for not responding earlier Have you tried alternative ways of setting up SUPPA? It may be easier to simply download the current version of the code. Thanks Eduardo On...

Could you share a sample of the GTF file you use as input and your command line? This problem is usually an issue with the format of the GTF or...

Please copy-paste few lines of data and the command line into the github window. I don't have a way to activate the html viewing Thanks E/

Please look at our papers https://pubmed.ncbi.nlm.nih.gov/26179515/ https://pubmed.ncbi.nlm.nih.gov/29571299/ They contain information on how to obtain the expression files. In our wiki tutorial there is more info: https://github.com/comprna/SUPPA/wiki/SUPPA2-tutorial I hope this helps...

Hi Joanna, It will be partly solved if you use the same annotation for the fasta and for the GTF It could be that there are many transcripts with zero...

Hi Jiehui, thanks for your interest in SUPPA As SUPPA uses the annotations, U12 introns that are included in the annotation will also be used for the SUPPA analysis. There...