SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Pipeline to simulate short reads and call indels pmaugeri Bioinformatics 17 03-01-2012 03:45 PM
Using MAQ to simulate illumina pair-end reads yjx1217 Bioinformatics 0 10-27-2011 08:38 AM
Simulate Illumina read-pairs gene coder Bioinformatics 4 07-07-2011 03:37 AM
Simulated reads mapping to same region - maq simulate & dwgsim gprakhar Bioinformatics 2 02-18-2011 11:12 PM
Simulate ABI reads wesb SOLiD 0 12-04-2008 09:10 AM

Reply
 
Thread Tools
Old 07-06-2011, 11:57 PM   #1
gene coder
Member
 
Location: Ireland

Join Date: Jul 2011
Posts: 18
Default dwgsim to simulate Illumina reads

Hello, I want to use dwgsim to simulate Illumina reads from the 1000 Genomes Project. I am particularly interested in individual NA12878.

Does anybody know what settings are (approximately or exactly) correct when it comes to the flags -e, -E, -r -R, -X and -Y (http://sourceforge.net/apps/mediawik...ome_Simulation)? Do you know where I can find technical details (does Illumina publish that?) so I can guess myself.

Can anybody explain those flags to a novice? Sequencing is not my domain.
gene coder is offline   Reply With Quote
Old 07-07-2011, 09:51 AM   #2
nilshomer
Nils Homer
 
nilshomer's Avatar
 
Location: Boston, MA, USA

Join Date: Nov 2008
Posts: 1,285
Default

Do you have someone who has an Illumina machine that you could ask for typical settings for -e and -E (base error rate)? For human, the rate of mutation (SNPs) is 1/1000, while for indels it is ~1/10000.

If you are using this tool, sequencing is your domain. -e/-E are the per base mean error rate, -r is the rate of mutation, -R is the fraction of mutations that are indels, and -X controls the indel length distribution (probability of extending an indel).
nilshomer is offline   Reply With Quote
Reply

Tags
1000 genomes project, illumina sequencing, simulation

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 10:12 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO