SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq and non-raw counts (but also not rpkm normalized) wingless Bioinformatics 0 06-26-2015 11:11 AM
Getting normalized counts IsBeth Bioinformatics 2 05-31-2014 09:20 AM
edgeR mean normalized reads counts for each gene antoza Introductions 2 02-11-2014 08:22 AM
converting bam files to non-normalized read counts lpn Bioinformatics 4 10-09-2012 07:52 PM
DESeq: Read counts vs. BP counts burkard Bioinformatics 0 08-05-2010 11:52 PM

Reply
 
Thread Tools
Old 07-03-2015, 03:48 PM   #1
friducha
Junior Member
 
Location: UK

Join Date: Jan 2015
Posts: 9
Default Start analysis from DESeq2-normalized read counts?

Hi all,

I know that DESeq2 relies on using raw read countsd as input. However, I have the following question:

What if the read counts were already normalized using DESeq2? Is there a way to start the analysis after this step?

A colleague did an initial DESeq2 run on our data, and supplied a table with the normalized read counts from DESEq. I do not have the raw counts, and was wondering if I could start from here and skip the normalization method that DESeq perfoms.
friducha is offline   Reply With Quote
Old 07-04-2015, 05:40 AM   #2
Michael Love
Senior Member
 
Location: Boston

Join Date: Jul 2013
Posts: 333
Default

For DESeq2, you shouldn't use any kind of values where the library size has been divided out. The statistical methods use the properties of the sampling distribution of counts, as well as estimation of additional variation (dispersion), for inference.

The input matrix should be: the number of reads/fragments which can be uniquely assigned to a gene (aligning to any of the exons of a gene).
Michael Love is offline   Reply With Quote
Reply

Tags
deseq, deseq2, rna-seq, rnaseq, sequencing

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 06:26 PM.


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