Go Back   SEQanswers > Bioinformatics > Bioinformatics

Similar Threads
Thread Thread Starter Forum Replies Last Post
Control-FREEC: a tool for assessing copy number and allelic content using NGS data valeu Literature Watch 77 04-23-2020 12:50 PM
Copy number analysis using 454 data ps376 Bioinformatics 3 10-08-2011 05:56 AM
PubMed: Control-free calling of copy number alterations in deep-sequencing data using Newsbot! Literature Watch 0 04-08-2011 02:10 AM
PubMed: Expression Analysis of miRNAs and Highly-expressed Small RNAs in Two Rice Sub Newsbot! Literature Watch 0 10-28-2010 03:30 AM
deepBase: annotating and discovering small and long RNAs from deep sequencing data rnaNGS RNA Sequencing 1 01-03-2010 06:22 AM

Thread Tools
Old 03-26-2011, 01:44 AM   #1
Senior Res.
Location: Plovdiv, Bulgaria

Join Date: Oct 2008
Posts: 110
Default way to normalize copy number data for small RNAs/miRNAs?

Hi all,
I have searching for a method for normalization if I want to do a diff. expression comparison on 4 datasets from illumina small RNAs(2 controls and 2 samples).
Is there a way to do a normalization and compare them or just to do a copy number comparison and calculate folds?

I have tested several tools for miRNA, but most of them do not provide a way for multiple compareson (maybe only mirTools). In other way what is the obligatory step so the diff. expression of the copy numbers to be accepted in papers?

vebaev is offline   Reply With Quote
Old 03-28-2011, 12:23 AM   #2
not just another member
Location: Belgium

Join Date: Aug 2010
Posts: 264

DESeq or edgeR package in R.

you can compare two groups of samples. It take as input a read count matrix (each line for a miRNA and each column for a sample ).
NicoBxl is offline   Reply With Quote
Old 03-28-2011, 03:18 AM   #3
Junior Member
Location: Geneva, Switzerland

Join Date: Sep 2010
Posts: 9

You can also have a look on bayseq...

These packages have methods to normalize counts... But you can also use RPKM... Or use your proper normalizator (total counts per instance)
Claudia34 is offline   Reply With Quote

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 11:08 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO