Jonathan Göke

HI @KrisJanssen the open access link is here: https://rdcu.be/cyjRN. We included the link in the [readme](https://github.com/GoekeLab/bioinformatics-workflows#about-this-repository) and [Discussions](https://github.com/GoekeLab/bioinformatics-workflows/discussions/22) so this should be easy to find. It's a good idea to...

Thanks for the suggestion @johanneskoester I very much like the idea! Do you have any example github page that you have in mind for this? Something along these lines here...

> I'm interested, but I can probably start in mid November. No problem at all, I think this would be a tremendous contribution!

I would suggest to keep things simple and just use `goekelab.github.io/bioinformatics-workflows`? The main landing page is https://github.com/GoekeLab/bioinformatics-workflows as that is printed in the review, so this github page would be...

Hi @cathoderaymission thanks for the detailed description, we will reply shortly with more details. In the meantime I wanted to ask if you can raise separate issues for (1), (2),...

Hi @cathoderaymission regarding your main issue here, can you run xPore with the reads that are aligned to the transcriptome reference instead of the genome reference and check if these...

Hi @cathoderaymission I would suggest to run xPore with the recommended options first, and f that still returns results which do not cover the expected coordinates, you could post a...

> Hi @jonathangoeke, > I have a question. I noticed in https://github.com/GoekeLab/xpore/blob/master/xpore/scripts/dataprep.py line 117: > > ``` > cond_successfully_eventaligned = eventalign_result['reference_kmer'] == eventalign_result['model_kmer'] > if cond_successfully_eventaligned.sum() != 0: > ```...

Hi @cathoderaymission have you tried aligning the data to the yeast transcriptome? Ensembl probides such files for example here: http://ftp.ensembl.org/pub/release-104/fasta/saccharomyces_cerevisiae/?

Hi @lwlive thanks for the question, can you post this to the [discussions](https://github.com/GoekeLab/xpore/discussions)? I will reply there