SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Mate pairs in ABySS VNou Bioinformatics 0 06-29-2012 07:57 AM
Fixing mate pairs in fastq lukas1848 Bioinformatics 2 05-03-2012 12:08 PM
Merging mate pairs by quality Yrinky Bioinformatics 2 04-13-2012 02:48 AM
Read length for Illumina mate pairs Linnea Illumina/Solexa 2 06-09-2010 12:46 AM
454 mate pairs and mosaik afb Bioinformatics 4 04-02-2010 06:07 AM

Reply
 
Thread Tools
Old 09-11-2012, 08:05 AM   #1
ChrisAU
Junior Member
 
Location: Tübingen

Join Date: Jan 2012
Posts: 9
Default dwgsim illumina mate pairs

Hi there,

I want to simulate Illumina mate pairs and thought of using dwgsim.
However, the manual states that it will create mate pairs, that have --> --> orientation, whereas Illumina mate pairs should have <-- --> orientation.
Am I wrong, or does dwgsim simulate only 454 and Solid mate pairs?

Thanks
Chris
ChrisAU is offline   Reply With Quote
Old 09-12-2012, 03:02 PM   #2
swNGS
Member
 
Location: SW UK

Join Date: Nov 2011
Posts: 83
Default

No, it can do Illumina format Fastas. Remember that with dwgsim you won't get any simulated quality info though
swNGS is offline   Reply With Quote
Old 09-14-2012, 12:51 AM   #3
ChrisAU
Junior Member
 
Location: Tübingen

Join Date: Jan 2012
Posts: 9
Default

It worked fine for paired-end reads, but not for the mate pairs.
Reverse complementing the first read should do the trick though. For the quality string, I just replaced the default quality string with the values from an average fastqc evaluation.
ChrisAU is offline   Reply With Quote
Reply

Tags
dwgsim, illumina, mate pairs, 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 05:53 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2021, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO