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

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 IsoformSwitchAnalyzeR. The error is shown below:

Step 1 of 2: importing GTF (this may take a while)…
Step 2 of 2: Adding ORF…
Error in addORFfromGTF(SwitchList, removeNonConvensionalChr = args$removeNonConvensionalChr, :
No ORFs could be added to the switchAnalyzeRlist. Please ensure GTF file have CDS info (and that isoform ids match).

To my knowledge StringTie does not output CDS, only “transcript” and “exon”, is this causing the error? Can you please advise the best approach to rectifying this?

The GTF file is from Ensembl and does have CDS in the input :slight_smile:
However the annotation generated by StringTie/StringtieMerge do not contain any CDS.
It’s being run on the Galaxy Au server.

Please let me now if I can add any more info :slight_smile:

Thanks so much for your advice,

Anna

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.