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  • 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

  • #2
    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; 02-10-2011, 12:22 AM.

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    • #3
      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

      Comment


      • #4
        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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        • #5
          hi brachysclereid,

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

          Thanks,
          Joji

          Comment

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