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-   -   fold change value-cuffdiff (http://seqanswers.com/forums/showthread.php?t=9350)

madsaan 02-09-2011 06:33 AM

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

dnusol 02-09-2011 11:15 PM

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?

madsaan 02-10-2011 05:24 AM

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

brachysclereid 02-10-2011 06:07 AM

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";


madsaan 02-10-2011 06:51 AM

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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