Cuffmerge error: duplicate/invalid 'transcript' feature ID=Ma03_t01040.3

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.

1 Like

Hi @tikshana_yadav

Some gff3 datasets are released by data providers that contained duplicated “ID” identifiers. These cause problems with almost all tools. Using gtf annotation is a better choice.

Please note that the tools you are using are deprecated. Details, reasons, and alternatives are covered in this prior Q&A:


Thank you for your kind information. Can you please suggest me some tools to get differential expression of genes in Musa balbisiana with non replicated data which has to annotated with Musa accuminata

Thank you all for your kind help. I simply want to suggest the future that if this sort of error will occur just check whether your input file is correct or not go through each and every location and check the path as well as your file name. Just keep everything simple do not complex anything. This is what I resolved these days. A small mistake in your command may hamper your time and experiment.

In short my bam file in samtools was not created properly so I run all command again and checked my path that resolved my issue/error. If you face the same just go through it make it SIMPLE