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  • Error message in cuffcompare

    Hello,

    I am trying to run cuffcompare with the transcript_GTF file from cufflinks but I get this error message:
    Error: no ID found for GFF record start
    Could you please help me with this? Thanks!!

  • #2
    I'm running cuffcompare with the same problem. I think that the problem is in the GTF-file but I'm not really sure. Do you know how to do?

    Thanks for your aid.

    Originally posted by Line View Post
    Hello,

    I am trying to run cuffcompare with the transcript_GTF file from cufflinks but I get this error message:
    Error: no ID found for GFF record start
    Could you please help me with this? Thanks!!

    Comment


    • #3
      Hello,

      If it can help, I ran Cuffcompare with this command line :
      cuffcompare -r /path/both.reference.alternative.isoform.gff -V -R /path/Cufflinks/L2/transcripts.gtf
      where transcripts.gtf is one of the output files of Cufflinks and both.reference.alternative.isoform.gff is like this :


      Code:
      ##gff-version	3
      DS571145	alternativeSplicer	gene	3484	4143	.	-	.	ID=EHI_151170;Name=hypothetical protein;
      DS571145	alternativeSplicer	mRNA	3484	4143	.	-	.	ID=EHI_151170.ref;Name=EHI_151170.ref;Parent=EHI_151170;completeORF=yes
      DS571145	alternativeSplicer	exon	3484	4143	.	-	.	ID=exon_EHI_151170.ref-1;Name=exon;Parent=EHI_151170.ref;
      DS571145	alternativeSplicer	mRNA	3484	4143	.	-	.	ID=EHI_151170.alt1;Name=EHI_151170.alt1;Parent=EHI_151170;completeORF=no
      DS571145	alternativeSplicer	exon	3484	3943	.	-	.	ID=exon_EHI_151170.alt1-1;Name=exon;Parent=EHI_151170.alt1;
      DS571145	alternativeSplicer	exon	3997	4143	.	-	.	ID=exon_EHI_151170.alt1-2;Name=exon;Parent=EHI_151170.alt1;
      DS571145	alternativeSplicer	gene	4256	5944	.	+	.	ID=EHI_151180;Name=calcineurin catalytic subunit A putative;
      DS571145	alternativeSplicer	mRNA	4256	5944	.	+	.	ID=EHI_151180.ref;Name=EHI_151180.ref;Parent=EHI_151180;completeORF=yes
      DS571145	alternativeSplicer	exon	4256	5944	.	+	.	ID=exon_EHI_151180.ref-1;Name=exon;Parent=EHI_151180.ref;

      Comment


      • #4
        Bump having this problem too

        Comment

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