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

Similar Threads
Thread Thread Starter Forum Replies Last Post
Single end read with paired end reads tahamasoodi Bioinformatics 2 01-16-2016 07:46 AM
Quality drop in the Reverse read of paired end library (illumina Hiseq 1000) anurupa Illumina/Solexa 2 10-21-2013 10:40 PM
Downstream analysis with Single end and Paired end with Hiseq dhanapala RNA Sequencing 4 06-08-2012 09:08 AM
searching 454 (single read) + Illumina paired-end or matepair data boetsie General 0 10-04-2010 01:45 AM
Difference in paired-end and single-end read ? darshan Bioinformatics 1 09-30-2009 11:44 PM

Thread Tools
Old 03-19-2015, 08:44 AM   #1
Junior Member
Location: Chicago, IL

Join Date: Jun 2014
Posts: 3
Default Confusion about single end vs paired end read output on Illumina HiSeq


I think I'm confused about read output for Illumina's HiSeq. I think I'm not understanding why it is possible to get 150M single end reads in a run, but you can get 300M pairs (is this double the data)? So what is the maximum number of TOTAL reads you can get (either on rapid-run or high-output).
I'm trying to understand multiplexing better. Because multiplexing is based on how many reads you desire, you determine how many libraries you can load in a single lane based on the max output (~140-150M reads) of a lane.
So say I want 20M single end reads, I can load 6 libraries safely with some buffer room and reach 20M reads per library. But if you want paired end reads, how does this work say if I want 20M pairs (40M total) per library; can I still load 6 libraries and reach that output? Is this purely based on maximum data that can be produced or on the chemistry of the SBS reagents in single end vs paired end mode?
Any resources are greatly appreciated. Thanks!
acidcoated is offline   Reply With Quote
Old 03-19-2015, 08:56 AM   #2
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,091

Unique clusters is what you need to consider.

If you sequence only one end then you get 150M reads but if you sequence the other then you get 300M reads. Each unique cluster can generate n x 2 number of reads. Illumina tends to quote number of paired end reads in their specifications (so that corresponds to half the number of unique clusters being sequenced).

In example above you don't change the loading concentration but just sequence the other end of the fragment to get a pair of reads for each cluster.
GenoMax is offline   Reply With Quote

illumina, output, paired end, single end

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 04:17 AM.

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