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Old 07-12-2010, 02:37 AM   #1
Line
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Location: Germany

Join Date: Jul 2010
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Unhappy 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!!
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Old 08-24-2011, 03:39 AM   #2
Rodri
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Location: Valencia

Join Date: May 2011
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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 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!!
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Old 08-31-2011, 11:41 PM   #3
Jane M
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Location: Paris

Join Date: Aug 2011
Posts: 239
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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;
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Old 09-20-2012, 12:05 PM   #4
Aholton
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Bump having this problem too
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