Error: duplicate GFF ID 'ENST00000400518' encountered! [FAILED] Error: could not execute cuffcompare

Question

[PK]

Hi folks, When I run cuffmerge

I have used this command

cufflinks Version - cufflinks_2_2_1

cuffmerge -p 16 -o ~/RNA_HOME/cuffmerge/merged -g ~/RNA_HOME/refs/hg19/genes/genes_chr22_ERCC92.gtf ~/RNA_HOME/de_novo/assembly_GTF_list.txt

Error: duplicate GFF ID 'ENST00000400518' encountered! [FAILED] Error: could not execute cuffcompare

I am getting this type of error. I am using de-novo mode.What is the solution?.Help me

[GenoMax]

Please validate ("accept"/vote for answers that helped you on previous threads you have posted). It is good etiquette to acknowledge past assistance on Biostars.

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In this case the error is clear. You need to get rid of duplicate entries for that GFF ID in your GTF file.

Answer 1

[i.sudbery]

Could well be a GTF that is not sorted in the correct order. I don't know how the cufflinks parser works, but for many GTF parsers, duplicate IDs are detected by finding that exons the same ID are not all next to each other. This can happen if the file is sorted purely on chromosome and start position as transcripts from the same gene will be interleaved and overlapping genes will be interleaved. You get around this you would need to sort by gene_id, then transcript_id, then start position.