SEQanswers

Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa



Similar Threads
Thread Thread Starter Forum Replies Last Post
minimum depth of coverage for transfrag extension apadr007 Bioinformatics 6 05-15-2012 06:23 AM
Experimental design based on coverage needed bioseq Bioinformatics 1 06-01-2011 08:40 AM
mouse miRNA seq with SOLiD, help with coverage needed desperately! bisrat SOLiD 2 06-29-2010 02:37 AM
Minimum Coverage for ChIP-Seq & RNA-Seq canis Illumina/Solexa 7 07-17-2009 01:34 AM

Reply
 
Thread Tools
Old 03-22-2011, 02:41 AM   #1
Annettet
Junior Member
 
Location: Oslo

Join Date: Mar 2011
Posts: 1
Default What is the minimum coverage needed?

Hi, (my very firs post here on this helpful forum

I have performed an experiment where I have placed individuals (from the wild) into new a environment, then I have sampled the individuals at different time points. I also have controlls for all the time intervals (individuals taken out of its common environment and placed back to similar conditions).
My plan is to sequence the mRNA on Illumina, potentially on a HiSeq2000 (but there is also a GA2 available).

I would be happy to get some suggestions reagrding coverage depth needed in order to aim at a certain number of individuals per lane (trying keeping the cost down). I am interrested in detecting active genes during a specific period in a defined environment, and to then, compare between different time stages. My study organism has about 21 000 genes, with a total of about 36Mb, and the genome has been sequenced (so I have a refrence genome). My plan is to go with paired end reads, and 50 or 75 bp.

Thanks in advance, this is all very new to me so all suggestions are welcome
Annettet 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 04:47 AM.


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