SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Resources for miRNA Expression koneru_18 Bioinformatics 3 10-15-2013 06:05 AM
miRNA's expression normalization Giorgio C Bioinformatics 0 12-06-2011 11:54 AM
Mirna expression analysis moriah Bioinformatics 3 08-23-2011 02:46 AM
miRNA targets expression profiles Livi81 General 0 01-20-2011 06:34 PM
making miRNA libraries antoniou RNA Sequencing 4 06-15-2010 06:14 PM

Reply
 
Thread Tools
Old 01-27-2014, 05:12 AM   #1
foolishbrat
Member
 
Location: South East Asia

Join Date: Nov 2008
Posts: 44
Default How to measure miRNA expression from Illumina libraries

I have a 51 single-end reads generated with MiSeq using NEBNext Multiplex Oligos for Illumina.

The data is obtained from from blood serum miRNA.

The sample sheet looks like this:

Code:
IEMFileVersion,4
Investigator Name,FB
Experiment Name,WT10104
Date,11/27/2013
Workflow,GenerateFASTQ
Application,FASTQ Only
Assay,TruSeq Small RNA
Description,
Chemistry,Default

[Reads]
51

[Settings]
ReverseComplement,0

[Data]
Sample_ID,Sample_Name,Sample_Plate,Sample_Well,I7_Index_ID,index,Sample_Project,Description
HS130333-1,,,,RPI3,TTAGGC,,
HS130333-2,,,,RPI4,TGACCA,,
HS130333-3,,,,RPI5,ACAGTG,,
So it contain 3 files:
Code:
HS130333-1.fastq
HS130333-2.fastq
HS130333-3.fastq
My question is, if I want to measure the miRNA expression,
should I combine all the 3 files above, then map them before computing the expression?

OR map each of the above 3 files individually and then average the expression?
foolishbrat is offline   Reply With Quote
Old 01-28-2014, 05:49 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

I suggest you to map individually, because you get more statistical power for further analysis.
TiborNagy is offline   Reply With Quote
Old 01-28-2014, 08:45 AM   #3
RedLightPanic
Junior Member
 
Location: Catalonia

Join Date: Jan 2013
Posts: 9
Default

Hi foolishbrat,

I agree with TiborNagy that the best option is to map them individually and the compute the miRNA expression separately.

On the other hand, I also suggest you to apply some type of normalization before going further on the analysis of miRNA expression. Here) you'll find a survey of normalization methods for small RNA-Seq data.

Hope this helps
RedLightPanic is offline   Reply With Quote
Old 01-28-2014, 04:27 PM   #4
foolishbrat
Member
 
Location: South East Asia

Join Date: Nov 2008
Posts: 44
Default

Thanks a million both.
foolishbrat is offline   Reply With Quote
Reply

Tags
expression, illumina, mirna

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 10:22 PM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO