dwgsim illumina mate pairs

ChrisAU · 09-11-2012, 08:05 AM

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

swNGS · 09-12-2012, 03:02 PM

No, it can do Illumina format Fastas. Remember that with dwgsim you won't get any simulated quality info though

ChrisAU · 09-14-2012, 12:51 AM

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.

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

09-11-2012, 08:05 AM	#1
ChrisAU Junior Member Location: Tübingen Join Date: Jan 2012 Posts: 9	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

09-12-2012, 03:02 PM	#2
swNGS Member Location: SW UK Join Date: Nov 2011 Posts: 83	No, it can do Illumina format Fastas. Remember that with dwgsim you won't get any simulated quality info though

09-14-2012, 12:51 AM	#3
ChrisAU Junior Member Location: Tübingen Join Date: Jan 2012 Posts: 9	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.