SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA Seq normalization harshinamdar Bioinformatics 39 03-16-2013 02:12 AM
RNA-seq and normalization numbers zee Bioinformatics 52 12-12-2012 06:44 AM
RNA-Seq: GC-Content Normalization for RNA-Seq Data. Newsbot! Literature Watch 0 12-20-2011 03:00 AM
clarification of rna-seq normalization frymor Bioinformatics 3 08-06-2011 07:07 PM
Quantile normalization for RNA seq data? Boel Bioinformatics 3 03-26-2010 04:07 PM

Reply
 
Thread Tools
Old 04-17-2012, 02:00 AM   #1
mattia
Member
 
Location: Milano

Join Date: Aug 2011
Posts: 30
Default Best reads normalization in RNA-Seq

Hi, I'm analysing a bit of RNA-Seq data, in particular at the moment I try to compare the expression of genes in several conditions. To evaluate the expression value I used both FPKM value (Cufflinks v 1.3.0) and raw count (DESeq v 2.6). Due to the different number of reads of two samples (tipically about 10 million of reads!!), I suppose that I can't compare the value of a gene in this 2 samples; for example:

FPKM_1=1 (or count_1=1) & FPKM=100 (or count_2=100) could not mean that there are differences between two condition (the difference is in order of size of one hundred).

So, my question is: in the next step, do the software that perform differential analysis (like Cuffdiff or DESeq) allow for this difference?

Otherwise, What's the best way to solve this problem?

Thanks a lot.
Mattia.

Last edited by mattia; 04-17-2012 at 06:50 AM.
mattia is offline   Reply With Quote
Reply

Tags
cufflinks, deseq, fpkm, normalization, rnaseq

Thread Tools

Posting Rules
You may not post new threads
You may not post replies
You may not post attachments
You may not edit your posts

BB code is On
Smilies are On
[IMG] code is On
HTML code is Off




All times are GMT -8. The time now is 08:07 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO