[ddRAD] on removal of duplicate reads

skm · 07-03-2017, 10:48 AM

Hi All,

Is it advisable to remove duplicate reads from double digest RAD (ddRAD) data generated on Illumina Hiseq platform ?

Regards,
Krishna

nucacidhunter · 07-03-2017, 06:40 PM

ddRAD libraries has two types of duplicates:

1- PCR duplicates
2- duplicates rising from input genome equivalent used for dig-lig

As most of ddRAD protocols does not use UMIs, it is not possible to distinguish those.

Throughout analysis a minimum coverage is used to form stacks of RAD-tags, catalog and estimate zygosity for the called genotypes so duplicates should not be removed.

Similar Threads
Thread	Thread Starter	Forum	Replies	Last Post
duplicate reads removal	vasvale	Bioinformatics	19	01-08-2015 01:59 AM
duplicate read removal	gab0	Bioinformatics	14	10-02-2014 04:20 PM
duplicate reads removal for amplicon libraries?	ngseq	Illumina/Solexa	0	12-10-2012 01:50 PM
threshold for duplicate removal?	mard	Bioinformatics	2	03-21-2010 04:45 PM

07-03-2017, 10:48 AM	#1
skm Junior Member Location: india Join Date: Nov 2011 Posts: 5	[ddRAD] on removal of duplicate reads Hi All, Is it advisable to remove duplicate reads from double digest RAD (ddRAD) data generated on Illumina Hiseq platform ? Regards, Krishna

07-03-2017, 06:40 PM	#2
nucacidhunter Jafar Jabbari Location: Melbourne Join Date: Jan 2013 Posts: 1,238	ddRAD libraries has two types of duplicates: 1- PCR duplicates 2- duplicates rising from input genome equivalent used for dig-lig As most of ddRAD protocols does not use UMIs, it is not possible to distinguish those. Throughout analysis a minimum coverage is used to form stacks of RAD-tags, catalog and estimate zygosity for the called genotypes so duplicates should not be removed.