Does anyone know how to fix the following cuffmerge errors?
Initially I thought it's the "reference annotation" file that was not recognized (as I have gff in the history : GCF_000001635.24_GRCm38.p4_genomic.gff). However, when I wanted to switch the reference file to GTF ( Mus_musculus.GRCm38.81.gtf ), the dropdown window did not even recognize the gtf file.
People on other forums have tried to remove dup/invalid transcripts, but I do not know if that was a real fix or temporary fix. Any idea? Or where can I find more info about the potential fix? (cuffmerge website: http://cole-trapnell-lab.github.io/cufflinks/cuffmerge/index.html/ does not seem to provide the answers I am looking for).
[Fri Sep 25 18:01:42 2015] Preparing output location cm_output/ [Fri Sep 25 18:02:08 2015] Converting GTF files to SAM [18:02:08] Loading reference annotation. GFF Error: duplicate/invalid 'transcript' feature ID=id1128281 [FAILED] Error: could not execute gtf_to_sam