I’m following along the de novo transcriptome assembly Galaxy tutorial (De novo transcriptome reconstruction with RNA-Seq) with my own data. I’m stuck at the stringtie-merge step; I’m getting the following error message:
Error: could not any valid reference transcripts in /corral4/main/objects/6/5/e/dataset_65e2a2c5-762d-4f88-bec9-002deee1ae23.dat (invalid GTF/GFF file?)
Is this saying that none of the annotated sequences in my reference GTF file overlap or correspond with those in my Stringtie assembled transcripts?
So far, I’ve checked that the chromosome names are the same in the FASTA and gtf file and I’ve tried using both gtf and gff3 file formats for the reference annotation file.