SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
PhiX removal jamimo Illumina/Solexa 5 04-06-2015 05:50 AM
phiX removal lgiloteaux Introductions 3 10-02-2014 05:19 AM
less PhiX than you think? beardy_man Illumina/Solexa 1 11-08-2013 12:50 PM
PhiX contamination MoritzF Illumina/Solexa 3 08-06-2013 05:49 PM
V3 PhiX kthai Illumina/Solexa 0 04-01-2011 12:21 PM

Reply
 
Thread Tools
Old 09-19-2017, 03:31 AM   #1
Shrek
Junior Member
 
Location: italy

Join Date: Sep 2017
Posts: 1
Default Too much PhiX

What happens if you spike-in more PhiX than you thought? I had a good Read1 (Q30 of 87%) but very high PhiX alignment (60%) and very low Q30 in read 2 (only 39%). Is this caused by over clustering? Clustering density 800 with a V3 2x300
Shrek is offline   Reply With Quote
Old 09-19-2017, 04:07 AM   #2
nucacidhunter
Senior Member
 
Location: Iran

Join Date: Jan 2013
Posts: 1,080
Default

Cluster density up to 1400 is within v3 specification (https://www.illumina.com/systems/seq...fications.html) and Illumina's specifciation is based on PhiX library sequencing. Low Q30 value for R2 must have some other reasons and best to contact the Tech support for diagnosis.
nucacidhunter 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 08:07 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2017, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO