I have searched through all the threads on this topic and I have yet to find a reasonable explanation for why I continue to encounter this error. I have already run Cufflinks on my samples, but when I attempt to run Cuffmerge (cuffmerge -p 8 -g /scratch/sbag/Tikshana/BANANA/RAW/Mac.gff3 -s /scratch/sbag/Tikshana/BANANA/RAW/Mac_genome.fa /scratch/sbag/Tikshana/BANANA/cuff/assemblies_Macbal.txt -o /scratch/sbag/Tikshana/BANANA/cuff/Macbal_merge), I get the following error:
GFF Error: duplicate/invalid ‘transcript’ feature ID=Ma03_t01040.3
Error: could not execute cuffcompare
i could not understant how to resolve can you please explain me clearly.