Forum: Bioinformatics
12-20-2014, 01:48 PM
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Replies: 0
Views: 2,002
How to compare Trinity and Cufflinks results
Hi friends !
I'm trying to analyze the result of differentially expressed genes (DEGs) between the cufflinks (Cuffdiff ) and the Trinity (EdgeR). I know that in a de novo pipeline you can use...
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Forum: Bioinformatics
08-28-2014, 07:20 PM
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Replies: 0
Views: 2,726
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Forum: Bioinformatics
08-28-2014, 01:25 PM
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Replies: 0
Views: 1,963
Cuffdiff - NO TESTED isoform
Hi !
I have one question. Analysing one gene differentially expressed by Cuffdiff, i saw that all of your isoforms are not differentially expressed. BUT the isoform that makes the gene be...
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Forum: Bioinformatics
08-12-2014, 07:15 AM
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Replies: 4
Views: 1,424
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Forum: Bioinformatics
08-12-2014, 07:11 AM
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Replies: 12
Views: 3,834
Hi Han.
Cuffdiff don't make an output with...
Hi Han.
Cuffdiff don't make an output with FPKM per replciates. He has one output file where show exactly the FPKM per conditions. You only have to parse the file and divided them in samples that...
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Forum: Bioinformatics
08-12-2014, 06:58 AM
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Replies: 4
Views: 1,424
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Forum: Bioinformatics
08-12-2014, 06:38 AM
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Replies: 4
Views: 1,424
Expressed genes vs Expressed transcripts
I analyzed differential gene expression using Cuffdiff, but the number of genes expressed is smaller than transcripts expressed. Anyone can explain this?
In my mind, the number of transcripts...
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Forum: Bioinformatics
07-24-2014, 08:32 AM
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Replies: 12
Views: 3,834
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Forum: Bioinformatics
07-23-2014, 09:52 PM
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Replies: 12
Views: 3,834
Cuffdiff normalization using 2 conditions
Hi,
I have one doubt. In my project, i have reads from 2 conditions (Control/Infected) for leaf and root. I am using Cuffdiff to normalize the data and make differential gene expression, but i...
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