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Search: Posts Made By: lucasmiguel
Forum: Bioinformatics 12-20-2014, 01:48 PM
Replies: 0
Views: 2,002
Posted By lucasmiguel
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...
Forum: Bioinformatics 08-28-2014, 07:20 PM
Replies: 0
Views: 2,726
Posted By lucasmiguel
Best way to compare DEG between de novo pipeline and Cufflinks pipeline

Hi!

I would like to know your opinion about WHAT IS THE BEST WAY to compare DEG ( Differentialy Expressed Genes) between de novo pipeline ( Trinity ->RSEM(bowtie)-> EdgeR or DESeq ) and Cufflinks...
Forum: Bioinformatics 08-28-2014, 01:25 PM
Replies: 0
Views: 1,963
Posted By lucasmiguel
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...
Forum: Bioinformatics 08-12-2014, 07:15 AM
Replies: 4
Views: 1,424
Posted By lucasmiguel
Ok. Thanks dpryan, helped a lot.

Ok. Thanks dpryan, helped a lot.
Forum: Bioinformatics 08-12-2014, 07:11 AM
Replies: 12
Views: 3,834
Posted By lucasmiguel
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...
Forum: Bioinformatics 08-12-2014, 06:58 AM
Replies: 4
Views: 1,424
Posted By lucasmiguel
I defined that one gene is DE if he has FDR <=...

I defined that one gene is DE if he has FDR <= 0.05 (5%) and the same threshold for transcripts. It's wrong?

And yes, i meant larger than.

Thanks for replying, dpryan.
Forum: Bioinformatics 08-12-2014, 06:38 AM
Replies: 4
Views: 1,424
Posted By lucasmiguel
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...
Forum: Bioinformatics 07-24-2014, 08:32 AM
Replies: 12
Views: 3,834
Posted By lucasmiguel
Right, but Cuffdiff normalizes different when he...

Right, but Cuffdiff normalizes different when he has 4 conditions and 2 conditions, right? I think this is the cause of different values of DE genes.

Thanks for ur answer.
Forum: Bioinformatics 07-23-2014, 09:52 PM
Replies: 12
Views: 3,834
Posted By lucasmiguel
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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