SEQanswers

Go Back   SEQanswers > General



Similar Threads
Thread Thread Starter Forum Replies Last Post
DESeq, experimental design lmolokin Bioinformatics 14 06-12-2013 06:36 AM
Newbie - experimental design question enkia Sample Prep / Library Generation 10 03-20-2012 05:09 AM
Experimental Design: Which Kind of Replicate to Use? SamCurt RNA Sequencing 6 12-24-2011 10:35 AM
Help for experimental design ips RNA Sequencing 2 05-09-2011 03:47 PM
Multiplexing experimental design question. chadn737 RNA Sequencing 1 04-12-2011 04:18 PM

Reply
 
Thread Tools
Old 09-23-2013, 02:36 PM   #1
crh
Member
 
Location: tx

Join Date: Dec 2009
Posts: 46
Default RNASeq experimental design

All

Hope I can pick your collective wisdom/experience.

A collaborator is planning to carry out an RNASeq experiment and separately, a RIPSeq experiment, and is looking for guidance regarding reads required for both. The genome size is ~ 112.3 MB, and they are planning to use Illumina platform.

Questions:
How to calculate the number of reads required?

What is the fold coverage required for accurate gene expression values?

How many samples per lane to achieve the # reads required?

Better to get paired-end or is single read OK

Re: read length - as long as you can afford? or will shorter reads be OK


Any and all advice welcomed

Charles
crh is offline   Reply With Quote
Reply

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 10:29 AM.


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