Eduardo Eyras

Hi, thanks for the message. Have you tried removing the events with only nan's in the input file? I hope this helps E. On Wed, 29 Apr 2020 at 13:47,...

This seems to come from the Python library for clustering. I am wondering whether the are still some events with all nan in a given group of samples. Or whether...

Hi, If there is only one cluster the silhouette score cannot be calculated, as it relies on inter cluster distances Perhaps you can explore other parameters to see whether more...

Hi, In principle there should be no constraints. There are multiple ways in which you could use pacbio data: 1) map pacbio reads to the genome and use the mappings...

Dear Yanshan, thanks for your email. And thanks a lot for testing the various options. I think you're operating correctly, but the problem may be in the transcript IDs. The...

Hi Yanshan, yep, supp diffSplice needs at least 2 samples per replicate to the test. Do you have reps to this? If you only have one rep per condition, there...

Hi, thanks for your message. You are right, SUPPA only identifies single intron retention events https://github.com/comprna/SUPPA#generation-of-transcript-events-and-local-alternative-splicing-events Even with the option for variable boundaries (-b V), it will probably only identify...

Alternatively, you can run SUPPA to study differential transcript usage (DTU). That will detect that relative change if it occurs between two or more conditions that you might be comparing....

Hi, thanks for your email if there is no expression data, or the transcripts in the denominator of the PSI formula have zero expression, the PSI output will be NA...

Hi, yes, it is the "-f" option in the psiPerEvent command I am wondering if python has a problem managing an ID with "-" on it? Does this happen to...