Go Back   SEQanswers > Sequencing Technologies/Companies > Illumina/Solexa

Similar Threads
Thread Thread Starter Forum Replies Last Post
ddRAD/GBS lib conc on HiSeq 3000/4000 ? BioGenomics Sample Prep / Library Generation 1 01-17-2017 02:12 PM
HiSeq 4000 : typical RAW data output in GBytes sklages Illumina/Solexa 9 09-17-2016 07:05 PM
HiSeq 4000 upgrade buthercup_ch Illumina/Solexa 4 07-27-2016 03:49 AM
SmartSeq2 on Illumina HiSeq 4000 StephanK Illumina/Solexa 1 07-12-2016 11:44 AM
HiSeq 3000/4000 2x150 data scrosby Illumina/Solexa 10 06-04-2015 09:29 AM

Thread Tools
Old 03-28-2017, 12:35 PM   #1
Senior Member
Location: USA, Midwest

Join Date: May 2008
Posts: 1,178
Default Realistic output for HiSeq 4000

The official spec for PF Clusters on the HiSeq 3000/4000 is 270-312M per lane. It seems that it is pretty easy to exceed this specification but I would like to ask regular operators of a 3000/4000 what PF cluster counts do you reliably get per lane? Is there a difference depending on library type?

kmcarr is offline   Reply With Quote
Old 03-28-2017, 01:49 PM   #2
Location: Livermore, CA

Join Date: Jan 2016
Posts: 45

It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.
misterc is offline   Reply With Quote
Old 03-28-2017, 04:30 PM   #3
Senior Member
Location: US

Join Date: Dec 2010
Posts: 458

Originally Posted by misterc View Post
It does depend on library type as well as insert size. I usually get 350-400M reads passing filter per FC.
Agreed. Long insert libraries (library molecules longer than 550 bp) will reduce yields and quality scores.
luc is offline   Reply With Quote
Old 03-28-2017, 04:41 PM   #4
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,101

Yield is not an issue as long as libraries have the right insert sizes. Illumina guidance is around 75% PF clusters for a good run.

There are optical duplicates but they appear to be randomly distributed when checked recently (n=1).
GenoMax is offline   Reply With Quote
Old 03-29-2017, 06:15 AM   #5
Devon Ryan
Location: Freiburg, Germany

Join Date: Jul 2011
Posts: 3,480

We usually get 300-400 million passing filter per lane on a HiSeq3000. "Optical" duplicates are typically below 10%, except with weird library types. Often the higher the read yield the lower the "optical duplicate" rate.
dpryan is offline   Reply With Quote

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 07:53 AM.

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