SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
HiSEQ flowcells/reagents compatibility ik76 Illumina/Solexa 1 01-09-2012 01:05 AM
Illumina Flowcells cystron Illumina/Solexa 1 06-14-2011 11:33 AM
BAD HiSeq flowcells BIG_SNP Illumina/Solexa 3 01-11-2011 08:05 AM
sequening reagents katy General 0 01-14-2010 11:51 AM
3.5 WFA using 3.0 reagents? pmiguel SOLiD 4 11-20-2009 11:05 PM

Reply
 
Thread Tools
Old 06-08-2011, 01:21 PM   #1
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default v3 Flowcells and Reagents?

Has anyone run the new v3 flowcells and reagents on the HiSeq2000? We need to purchase more reagents but I am hesitant to switch over without feed back from other people.
NextGenSeq is offline   Reply With Quote
Old 06-23-2011, 01:54 PM   #2
dhinerfeld
Member
 
Location: Bar Harbor, ME

Join Date: May 2008
Posts: 12
Default

We haven't but will be soon. As I understand it, V3 will soon be the only option from Illumina. I actually have a question about how much library to load on the V3 kits to get in the range of 800k clusters/mm^2. On the V2 flow cells, we get about 600K with 9pm loaded. We titrated the load on the V2 lanes and the resulting cluster densities increased linearly with the load, to a point. In moving to a larger lane, I don't think the same would be true. Does anyone have experience with this?
dhinerfeld is offline   Reply With Quote
Old 06-23-2011, 01:58 PM   #3
GW_OK
Senior Member
 
Location: Oklahoma

Join Date: Sep 2009
Posts: 411
Default

We'll be transitioning to v3 soon as well. Our FAS suggested starting at 12pM.
GW_OK is offline   Reply With Quote
Old 06-24-2011, 06:53 AM   #4
NextGenSeq
Senior Member
 
Location: USA

Join Date: Apr 2009
Posts: 482
Default

Note the optics of your HiSeq have to be recalibrated before running v3 flowcells and reagents. The Y coordinates in the config file needs updating by using a beaded flow cell by your service engineer.
NextGenSeq is offline   Reply With Quote
Old 06-27-2011, 12:07 PM   #5
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,062
Default

Something to make a note of: The quality table for the new, v3 kits has a range from “B” to “m" per Illumina tech support.
GenoMax is offline   Reply With Quote
Old 06-28-2011, 04:37 AM   #6
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,317
Default

So now the highest quality value is 45? What was it previously?

--
Phillip
pmiguel is offline   Reply With Quote
Old 06-28-2011, 04:41 AM   #7
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 7,062
Default

Quote:
Originally Posted by pmiguel View Post
So now the highest quality value is 45? What was it previously?

--
Phillip
It was 40 (http://en.wikipedia.org/wiki/FASTQ_format).
GenoMax is offline   Reply With Quote
Old 06-28-2011, 05:57 AM   #8
pmiguel
Senior Member
 
Location: Purdue University, West Lafayette, Indiana

Join Date: Aug 2008
Posts: 2,317
Default

Well the unavoidable cheap shot at Illumina is: kind of like having an amplifier that goes up to "11"?

Looks like the highest ordinal for a printable ascii char is "62" for "~". Roughly one error in 4 million base calls. For a 33 offset encoding you can reach a quality score of "93". One error in 8 trillion base calls.

--
Phillip
pmiguel is offline   Reply With Quote
Reply

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 03:29 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2020, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO