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Old 08-05-2011, 11:57 AM   #1
Paul Walker
Junior Member
Location: Minnesota

Join Date: Feb 2011
Posts: 3
Default cuffdiff for differential gene testing

I am using tophat, cufflinks, cuffcompare and cuffdiff to analyze 5 MZ twin pairs discordant for diabetes.
After the preliminary fastq groomer file conversion, the RNA-seq fastq paired end data files are run in tophat with reference HG19 genome to align the reads.
Cuffcompare is then run on the tophat files to compare twin pair transcripts.
Finally, cuffdiff is used first to compare individual twin pairs (tophat files)
with HG19 reference gtf which, generates unique NM ids, FPKM values, p
and q statistic values and fdr significances.
Then the groups replicate function is used to the combined diabetic and non-diabetic twins in 2 groups against the HG19 reference gtf.
This also, produces NM ids, etc.
From my reading of the documentation it appears the statistical test for replicates is similar a group comparison t-test. What I would like to run is a
combined paired t-test as the samples are MZ twins. I think I am ok with the
initial individual twins cuffdiff analysis but, suspect the combined replicates
is a group mean comparison rather then a combined paired comparison.
The documentation on cufflinks says not to use count-based differential gene
methods on the FPKM data. I am not sure this applies to the data after cuffdiff analyses as the spliced variants are separated after this analysis but, when I run a paired t-test on the extracted FPKM 5 twin pairs data I get quite different results.
What is going on?

Paul W.
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Old 03-07-2013, 09:08 PM   #2
Location: Pune

Join Date: Oct 2012
Posts: 15
Default answer for the same

Dear Sir,

Have you managed to get answer for this. We are looking for answer of similar question.

Thank you,
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Old 03-08-2013, 09:25 AM   #3
Paul Walker
Junior Member
Location: Minnesota

Join Date: Feb 2011
Posts: 3
Default paired t-test and differential gene testing

What I did was to use a 3rd party software called Gene Data Expressionist.
The GDE Genome Refiner module can be used with Tophat alignment bam or sam files. There are defined workflows for RNA-seq to do the transcript counting and generate FPKM normalized counts that can be used for statistical comparison testing.
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Old 03-11-2013, 07:10 PM   #4
Junior Member
Location: South Korea

Join Date: Mar 2013
Posts: 1

Dear all,

I have some output files from two rna seq conditions. e.g.

Since I am new in rna seq analysis and I am kind of lost. I will highly appreciate if I could get an idea where should i start to interpret these output files.


Last edited by adeel_malik; 03-11-2013 at 07:17 PM.
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Old 01-26-2015, 09:04 AM   #5
Location: London, UK

Join Date: May 2012
Posts: 16

Hi Paul

I was wondering whether you have published anything with this RNAseq data you have? Is the data publicly available yet>?

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