Hi everyone i post my situation because i have this error:
GFF Error: duplicate/invalid 'transcript' feature ID=PHASIBEAM10F001038T1 [FAILED]
I asked here before and answered me delete the duplicated values, so i think that these duplicated values are in my gff3 file in the annotation of genome. So i reviewed my genome annotation and i found that the CDS features are duplicated. Just for see if it works, i erase the CDS features, and it worked for a time, but when i make cuffdiff assay the program returns me empty values. So the CDS are necessary, and make cuffdiff works, i thought. Well if the duplicated value is not in my annotation value maybe is in the cufflinks file, so i downloaded one file (assembled_transcripts gtf) and look for these duplicated values in the report error. when i find these values, appear something like that:
If look in the image exist 2 transcripts with the same id (two transcript feature in the top)
transcript_id "PHASIBEAM10F001285T1"
But one have the gene_id and the other not. Looking in the gff3 gene annotation just exist one transcript with the name transcript_id "PHASIBEAM10F001285T1" and have 3 exons like in the transcript with gene_id lack. These happen with some transcripts and not happen with the rest, i don't know why these transcripts have this error and the others not. i don't know if it's a cufflinks error, if is a wrong setting in TopHat/cufflinks protocol, or is the annotation genome format. Please if anyone know what it's happen please answer me. My best regards Claudio
