Eduardo Eyras

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,...

Hi Fairlie, thanks for your email, and for investigating already some of the potential issues. I think the problem is the sparse data. That error is common when SUPPA cannot...

Hi, these must be transcripts in the annotation that are not expressed and do not have an entry in the expression file. Did you check that your PSI file is...

Hi, I am wondering, is suppa.py in your path? Your command does not call python. It could also be that it is not using python3.4? The input files seem ok....

Hi, If you run each command separately, outside the bash loop, do you get the same error for all $base and $f files? Or for some of them? That error...

Hi, were you able to find where suppa.py is? Maybe JC or Miha can help you with the Windows installation Best Eduardo On Thu, 16 Apr 2020 at 13:17, namansep...

Hi Lina, thanks for your message. The pip install is probably not up-to-date. If you clone or download the latest version of the software it should work fine Sorry about...

Hi, Have you tried running the command with a python call? python3.4 ~/SUPPA/suppa.py generateEvents -i Homo_sapiens.GRCh38.103.gtf -o tEvents -f -ioe It should work as long as the server allows you...

Hi, It seems that the annotation has only one transcript per gene: awk '$3=="transcript"' Bombyx_mori.ASM15162v1.49.gtf | cut -f9 | cut -f2 -d" " | sort | uniq -c | awk...

Hi, SUPPA relies on a transcriptome annotation to do the alternative splicing analysis. However, it does not have to be only the Ensembl annotation. If you have Illumina RNA-seq, you...