SEQanswers

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



Similar Threads
Thread Thread Starter Forum Replies Last Post
deNovo assembly. High percentage of improper pairs. biojl RNA Sequencing 0 11-20-2013 07:26 AM
High duplication percentage klebsiella Illumina/Solexa 2 01-17-2013 04:45 AM
High percentage of N calls in the library apredeus Bioinformatics 2 12-08-2012 03:27 PM
Transcriptome Unclassified Blast Query Giorgio C Bioinformatics 0 10-28-2010 07:41 AM
ChIP-seq of possibly high repeated sequences dawe Epigenetics 8 09-10-2009 11:04 AM

Reply
 
Thread Tools
Old 11-29-2013, 09:23 AM   #1
Volunteer42
Junior Member
 
Location: Washington

Join Date: Nov 2013
Posts: 1
Default high percentage of unclassified sequences on Illumina

Hi all,
I'm sequencing V6 region of bacterial 16S on an Illumina MiSeq and when I got my sequences back and process them using mothur, I'm getting a LOT of unidentified sequences. Like maybe 50% for some samples in the run. This wasn't the case for other Illumina runs on similar samples. Any ideas on what the cause may be? Is it appropriate to just remove these unidentified sequences from further analysis and publication or not? Your help is greatly appreciated.
Volunteer42 is offline   Reply With Quote
Old 11-29-2013, 12:46 PM   #2
thomasblomquist
Member
 
Location: Ohio

Join Date: Jul 2012
Posts: 68
Default

QIIME pipeline a subset of your reads. A few "OTU" consensus sequences will come from this. Blast then against the NCBI nucleotide database and you'll have a general idea if it's technical artifact, an odd variant of your target of interest, or something completely different. -Tom
thomasblomquist is offline   Reply With Quote
Old 11-29-2013, 02:01 PM   #3
bilyl
Member
 
Location: USA

Join Date: Aug 2013
Posts: 52
Default

FastQC will also give you a quick and dirty check of any "overrepresented" sequences. Depending on what you're trying to do, you might be picking up a lot of eukaryotic contamination or Illumina adapter dimers.
bilyl 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 03:23 PM.


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