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Line 07-12-2010 02:37 AM

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!!

Rodri 08-24-2011 03:39 AM

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.

Quote:

Originally Posted by Line (Post 21667)
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!!


Jane M 08-31-2011 11:41 PM

Hello,

If it can help, I ran Cuffcompare with this command line :
Quote:

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;


Aholton 09-20-2012 12:05 PM

Bump having this problem too


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