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institut-de-genomique / Gmove

Gmove is a gene prediction tool
http://www.genoscope.cns.fr/gmove
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Increase number of UTRS #2

Open chklopp opened 3 years ago

chklopp commented 3 years ago

I've tested gmove on a plant genome and get a correct busco score ~ 93% of complete for the provided transcripts. The number of generated UTRs is very low. 160288 CDS 34152 mRNA 1569 UTR

I did not provide a file for the --annot parameter and non of the 3 other inputs has UTRs tags. How could I increase the UTR count?

auryjm commented 3 years ago

Could you specify the type of input parameters you used (rna, prot, annot, ....). Theorically, UTRs can only be predicted when using the --rna parameter (because in this case the start and stop codon are unknown).

chklopp commented 3 years ago

Here is my command line gmove -f Eukaryota.dna.masked.fa --rna cufflinks_aln.gff --prot exonerate_aln.cleaned.gff --abinitio braker_augustus.cleaned.gff3

auryjm commented 3 years ago

OK, it should work that way. Do you find examples of complete RNAs that did not lead to the prediction of UTRs ? It is difficult to know if there is a problem because we do not know here what to expect. If you find such an example and share the corresponding gff lines from the region, I can check.