Maximum insert size with Hiseq 3000

upendra_35 · 07-20-2015, 12:31 PM

What is the maximum size of insert allowed/optimum in Hiseq 3000? For one of our analysis, we needed a longer insert size (~800bp) which is ok in the case of 2000 but i was told that it is not good in the case of 3000. Can anyone comment on this?

NextGenSeq · 07-21-2015, 09:04 AM

Anything over 500 bp is not recommended.

andibody · 07-22-2015, 07:45 AM

I heard fragments from 400bp on or even below would start causing problems?

luc · 07-22-2015, 01:30 PM

Please see:
http://dnatech.genomecenter.ucdavis....data-download/

andibody · 07-23-2015, 04:20 AM

If the size bias is so extreme, does it mean that applications with non-random insert sizes shouldn't be run on the HiSeq3000/4000 at all?

GenoMax · 07-23-2015, 04:25 AM

This thread has some useful information about data characteristics from that HiSeq 3000 dataset linked above: http://seqanswers.com/forums/showthread.php?t=58353

andibody · 07-23-2015, 04:44 AM

Thanks for the link!

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07-20-2015, 12:31 PM	#1
upendra_35 Senior Member Location: USA Join Date: Apr 2010 Posts: 102	Maximum insert size with Hiseq 3000 What is the maximum size of insert allowed/optimum in Hiseq 3000? For one of our analysis, we needed a longer insert size (~800bp) which is ok in the case of 2000 but i was told that it is not good in the case of 3000. Can anyone comment on this?

07-23-2015, 04:25 AM	#6
GenoMax Senior Member Location: East Coast USA Join Date: Feb 2008 Posts: 7,088	This thread has some useful information about data characteristics from that HiSeq 3000 dataset linked above: http://seqanswers.com/forums/showthread.php?t=58353 Last edited by GenoMax; 07-23-2015 at 04:55 AM.

07-21-2015, 09:04 AM	#2
NextGenSeq Senior Member Location: USA Join Date: Apr 2009 Posts: 482	Anything over 500 bp is not recommended.

07-22-2015, 07:45 AM	#3
andibody Member Location: Vienna Join Date: Mar 2008 Posts: 45	I heard fragments from 400bp on or even below would start causing problems?

07-22-2015, 01:30 PM	#4
luc Senior Member Location: US Join Date: Dec 2010 Posts: 453	Please see: http://dnatech.genomecenter.ucdavis....data-download/

07-23-2015, 04:20 AM	#5
andibody Member Location: Vienna Join Date: Mar 2008 Posts: 45	If the size bias is so extreme, does it mean that applications with non-random insert sizes shouldn't be run on the HiSeq3000/4000 at all?

07-23-2015, 04:44 AM	#7
andibody Member Location: Vienna Join Date: Mar 2008 Posts: 45	Thanks for the link!