SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
multiplexing 16 samples together ran on 4 lanes or multiplexing 4 samples per lane? zatoichi888 Sample Prep / Library Generation 5 03-30-2014 10:16 AM
Including virus samples in an exome run? lilletine SOLiD 2 05-01-2013 03:08 AM
GATK - RealignerTargetCreator ? need to run for all samples in the same experiment ? swNGS Bioinformatics 4 04-22-2013 12:52 AM
454Jr run metrics - possible PCR primer contamination NGS4YetiB 454 Pyrosequencing 0 08-18-2011 02:54 PM
16 lane run leakage TonyBrooks 454 Pyrosequencing 1 05-24-2010 09:05 AM

Reply
 
Thread Tools
Old 12-08-2013, 02:42 PM   #1
MLog
Member
 
Location: Russia

Join Date: Jan 2010
Posts: 36
Question Contamination between samples run on the same lane

Hi colleagues,
I found a strange effect when sequencing several samples on Miseq. The reads from each sample contain about ~0.1% of reads from other samples run on the same flowcell. This does not seem to be caused by improper recognition of barcodes - we did demultiplexing without allowing mismatches, and the indices are very different one from another (e.g. TAGCTT and AGTTCC).
And this is certainly not contamination during library preparation - because I had one of the samples sequenced twice, with different "neighbors" and the contaminating reads were different.
Have you ever seen something like that? What can be done to minimize this?
MLog is offline   Reply With Quote
Old 12-08-2013, 03:26 PM   #2
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,574
Default

See if your observation is the same as recently mentioned here: http://seqanswers.com/forums/showthread.php?t=38697
GenoMax is offline   Reply With Quote
Old 12-08-2013, 03:32 PM   #3
MLog
Member
 
Location: Russia

Join Date: Jan 2010
Posts: 36
Default

No, this is not a contamination between runs, if you mean this.
MLog is offline   Reply With Quote
Old 12-08-2013, 03:49 PM   #4
GenoMax
Senior Member
 
Location: East Coast USA

Join Date: Feb 2008
Posts: 6,574
Default

Check the posts by vl80 and JackieBadger in the thread I linked above. They are about cross contamination between samples in the same run. That is what you are referring to right?
GenoMax is offline   Reply With Quote
Old 12-08-2013, 05:42 PM   #5
mcnelson.phd
Senior Member
 
Location: Connecticut

Join Date: Jul 2011
Posts: 162
Default

Yeah, it looks like you're seeing what I've been calling index misassignment. It apparently stems from image alignment and signal bleed issues during index sequencing that causes a cluster to be assigned the wrong index sequence.

Unfortunately, nothing can really be done about it, although dual indexing will cut down on the misassignment issue.
mcnelson.phd is offline   Reply With Quote
Reply

Tags
contamination, illumina

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 01:14 AM.


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