Go Back   SEQanswers > General

Similar Threads
Thread Thread Starter Forum Replies Last Post
RNA-Seq Experimental Design Questions dbroh11 RNA Sequencing 11 02-04-2014 11:09 AM
RNA-Seq Experimental Design dbroh11 Introductions 3 01-31-2014 07:32 AM
CASIM: RNA-Seq Factors in experimental design casim UK - Cambridge 0 04-18-2013 12:15 PM
seeking pooled sequencing experimental design advice bluesquid General 0 08-13-2012 06:34 AM
seeking pool-seq experimental design advice bluesquid Genomic Resequencing 0 08-07-2012 04:15 AM

Thread Tools
Old 01-29-2019, 07:32 AM   #1
Junior Member
Location: Cambridge, UK

Join Date: Feb 2017
Posts: 2
Default Advice RNA-Seq experimental design


I've recently started working in a group that would like to start doing RNA-Seq experiments in order to compare the transcriptomes of pancreatic islets undergoing different treatments.

As I'm new to this kind of work, I was wondering if anyone could offer advice on experimental design - specifically, how do you choose the correct number of samples (technical and biological replicates) and the depth of sequencing to give statistically meaningful results? Is it necessary to carry out a 'power' analysis to answer these questions? If so, how do you do that?

I've spent some time going through the literature on this, but frankly, it's quite confusing and seems inaccessible to anyone without a background in advanced maths or statistics. (I have neither.)

However, on the basis of what I've read, I've decided to run a pilot sequencing experiment with a limited number of samples and then enter the data into the 'Scotty' web-tool as described here:

This then returns information on number of samples and read-depth required to achieve a specific statistical 'power'.

Does that sound like a reasonable course of action?

Any advice on this matter would be much appreciated. In fact, any advice, or pointers to worthwhile reading material/resources in the area of RNA-Seq difference analysis would be a huge help.

Thanks for any advice offered.


john_gamble is offline   Reply With Quote

rna-seq advice, rna-seq beginner, rna-seq design

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 04:15 PM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO