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Old 08-31-2011, 11:41 PM   #3
Jane M
Senior Member
 
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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