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Old 02-10-2011, 06:07 AM   #4
brachysclereid
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Location: California

Join Date: Feb 2011
Posts: 32
Default Trouble with GTF in Cufflinks

Hi,
I have seen something similar to what you are reporting when the FPKM in one sample is zero. In this case you can't compute a log fold change, but I am sure that you would have spotted that...

I am having trouble getting Cufflinks to use my GTF also. Can anyone spot what's wrong with this? Everything looks ok to me, but I am just learning about this format:

HTML Code:
Un	protein_coding	exon	34432	34800	.	-	.	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "1"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI";
Un	protein_coding	CDS	34432	34800	.	-	0	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "1"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI"; protein_id "GSVIVT00013290001";
Un	protein_coding	start_codon	34798	34800	.	-	0	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "1"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI";
Un	protein_coding	exon	33789	34034	.	-	.	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "2"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI";
Un	protein_coding	CDS	33789	34034	.	-	0	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "2"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI"; protein_id "GSVIVT00013290001";
Un	protein_coding	exon	33058	33255	.	-	.	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "3"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI";
Un	protein_coding	CDS	33058	33255	.	-	0	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "3"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI"; protein_id "GSVIVT00013290001";
Un	protein_coding	exon	30354	30415	.	-	.	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "4"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI";
Un	protein_coding	CDS	30354	30415	.	-	0	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "4"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI"; protein_id "GSVIVT00013290001";
Un	protein_coding	exon	29264	29360	.	-	.	 gene_id "GSVIVG00013290001"; transcript_id "GSVIVT00013290001"; exon_number "5"; gene_name "D1J5D6_VITVI"; transcript_name "D1J5D6_VITVI";
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