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

Similar Threads
Thread Thread Starter Forum Replies Last Post
scaffolding GAII paired-end library with Hiseq mate-pairs stevebaeyen Bioinformatics 17 02-27-2013 02:45 AM
Anyone has protocol for Ion PES protocol? marcowanger Ion Torrent 1 01-18-2012 09:28 PM
Pacbio C2 chemistry dongyongdong Pacific Biosciences 3 11-15-2011 02:34 AM
SOLiD PE Chemistry Sophie Rose SOLiD 2 01-24-2011 10:58 AM
illumina alternative v1.5 protocol for small rna seq vs. the standard protocol ik76 Sample Prep / Library Generation 1 03-25-2010 03:24 PM

Thread Tools
Old 01-12-2012, 10:20 AM   #1
Junior Member
Location: USA

Join Date: Apr 2010
Posts: 1
Default Chemistry and protocol differences in Miseq, GAII and Hiseq?

Does anyone know any chemistry and protocol differences in Miseq, GAII and Hiseq? My amplicon-enriched libraries worked well in GAII and HIseq but not in Miseq in terms of mappable reads as well as amplification uniformity. They are same libraries using same barcodes and sequencing primers.

Thanks a lot
dwang is offline   Reply With Quote
Old 02-19-2013, 08:29 AM   #2
Junior Member
Location: Netherlands

Join Date: Feb 2013
Posts: 1

I wouldnt mind having an answer on this as well.
Karel is offline   Reply With Quote
Old 02-19-2013, 09:07 AM   #3
Senior Member
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,089

MiSeq has known problems with libraries that have low nucleotide diversity. There are several threads (an example thread: on SeqAnswers that address that issue. There are workarounds proposed but no definite solution as yet.

As for the answers regarding the chemistry used for the 3 platform and the differences search through these FAQ's.
GenoMax is offline   Reply With Quote
Old 02-19-2013, 09:49 AM   #4
Senior Member
Location: Boston,MA

Join Date: Nov 2008
Posts: 122

Also, the Tm for custom primers are different between HiSeq and MiSeq.

The HiSeq custom primer needs only to be above 56, where MiSeq must be above 66. It has to do with the difference in the annealing of the primer. We found that out the hard way!

Also, legacy (non-TruSeq) Single read libraries will not run on MiSeq. Another item we found out the hard way!
kwaraska 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 03:54 PM.

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