Hi there, I have been attempting to run genome -wide isoform analysis as per the Tutorial here: Hands-on: Genome-wide alternative splicing analysis / Genome-wide alternative splicing analysis / Transcriptomics I am using my own data. I have encountered a problem at the step of importing data to Is…

Hi @bellez34r3 Great, thank you! To help a bit with this, I also tried to run the tutorial data through the workflow and discovered a tiny wrinkle… the input data and workflow are not a perfect match, and a small adjustment is needed. This issue ticket contains all of the details → Suggested updat…

Welcome, @bellez34r3 That tutorial has several data preparation steps after the Stringtie step. Are you also doing those for your own data? If not, I would suggest starting there.

Hi Anna, I hope you are very well! I am doing the same pipeline as you and I encountered the same problem, were you able to add CDS to the StringTie output or what was the path you followed to solve this issue? I hope you can help me thank you very much

Welcome, @Carina_RCh (and @bellez34r3 can still reply of course!) As far as I know, the error reported above can be due to not using a reference annotation with Stringtie. Specifically, the tool is trying to match up transcript identifiers aka “isoform ids” between the different input files. What i…

Hi Jennaj Thanks for replying… In my case, as a reference annotation I am using the output of the StringTie merge described in this pipeline step: [image] Transcriptomics / Genome-wide alternative splicing analysis / Hands-on:... Training material for all kinds of transcriptomics anal…

Hi all, Apologies for the delay in replying. I also tried following the steps. It was ok when making transcript coordinates, reference transcriptome annotation, and transcriptome quantification with StringTie. I am yet to find a solution. I haven’t been able to get past the “import data” step in …

Hi Jenna, In my case I have used a reference GTF file (Ensembl) as the guide for assembly in StringTie. I checked and it does have CDS features, however the “assembled transcript coordinates” generated with StringTie has no CDS in the output. Is there a reason this is lost during transcriptome asse…

Hi @bellez34r3 Stringtie is a discovery tool, and it doesn’t call (or annotate) newly predicted coding regions in discovered transcripts. See the process at this specific step in the tutorial you referenced. https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/dif…

Thank you! I think for sure I will run through the process with the data provided for the tutorial itself so I can get a handle on the inputs and outputs at each step. Then I can try and narrow down where the issue is :slight_smile: Thanks so much for your help. If I come up with a solution after …

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Genome wide alternate splicing analysis - IsoformSwitchAnalyzeR error from StringTie input - no CDS