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Old 02-09-2011, 06:33 AM   #1
madsaan
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Question fold change value-cuffdiff

Hi,

I am trying to find the fold change between male and female gonad using cuffdiff.it seems to be working fine but am getting a value of -1.79769e+308.Now I need to find the top ten up and down regulated gene but not able to so because of the above value which appears for a significant number of genes.any help will be greatly appreciated.

Thanks,
Joji
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Old 02-09-2011, 11:15 PM   #2
dnusol
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Hi Joji,

If I am not wrong, the ln(fold_change) column in the gene_exp.diff file shows what you are after.
By the way, did you manage to get gene information-annotation for your results using a genome .gtf file?

Last edited by dnusol; 02-09-2011 at 11:22 PM.
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Old 02-10-2011, 05:24 AM   #3
madsaan
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thanks dnusol for your reply.I used a gene annotation.gtf file for cuffcompare.I am getting -1.79769e+308 in the ln(fold change) column so quite confused.

Thanks,
joji
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Old 02-10-2011, 06:07 AM   #4
brachysclereid
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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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Old 02-10-2011, 06:51 AM   #5
madsaan
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hi brachysclereid,

You should put a chr in front of Un and other chromosome numbers as well.it should work after that.

Thanks,
Joji
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