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Old 04-18-2011, 10:54 PM   #1
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Default control and test in DE in RNA-seq

I have been analyzing the mRNA-seq data using Cuffdiff and has two questions:

1. In case of Differential expression analyis between a control vs test sample, ln fold change is represented as Value2/ Value1 as per the manual of Cufflink. I was wondering Value 1 should be control while Value 2 should be test sample.
From Cufflink manual:
FPKMx 8.01089 FPKM of the gene in sample x
FPKMy 8.551545 FPKM of the gene in sample y
ln(FPKMy/FPKMx) 0.06531 The natural log of the fold change y/x

2. In typical control vs test sample based on Hg19 reference annotation- I get around 36K transcripts (total including no test and test OK) that seems to be little less as expected. Does it seem to be right number?

3. When I combine/ filter combined GTF file with any of isoform.exp file I get
RIC8A chr11:202907-236320 OK chr11 207163 208938 exon 1
RIC8A chr11:202907-236320 OK chr11 209271 209318 exon 2
RIC8A chr11:202907-236320 OK chr11 209407 210000 exon 5

Here the combined GTF provide a location (in red) Chr11 202907-236320 while cufdiff provide exon spanning 207163 208938. What is the first location refer to It is referring to neither gene location nor longest transcript. Any suggestion please.

Last edited by honey; 04-18-2011 at 10:56 PM.
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Old 04-19-2011, 10:04 PM   #2
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Default Question

Any suggestion please.
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