Cuffmerge Error Duplicate Transcripts
i want to merge cufflinks transcript.gtf files into a single file using cuffmerge the reference genome was downloaded from gencode am getting this error ...
GFF Error: duplicate/invalid 'transcript' feature ID=ENST00000361547.6
[FAILED]
Error: could not execute cuffcompare
rna-seq
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finswimmer
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yaminivadapally •
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