Go Back   SEQanswers > Applications Forums > Metagenomics

Similar Threads
Thread Thread Starter Forum Replies Last Post
High number of optical duplicates on MiSeq mareen_engel Illumina/Solexa 4 02-06-2015 12:34 AM
Number of clusters are way too high in my QIIME analysis nouse Illumina/Solexa 2 01-21-2015 11:29 AM
deNovo assembly. High percentage of improper pairs. biojl RNA Sequencing 0 11-20-2013 08:26 AM
High number of N in reads papori Illumina/Solexa 3 01-22-2013 06:21 AM
Cufflinks v 1.2.0 high number of RPKM 0 hlwright Bioinformatics 1 11-30-2011 08:08 AM

Thread Tools
Old 06-01-2015, 03:21 AM   #1
Location: Hong Kong

Join Date: Jun 2014
Posts: 13
Default high number of denovo OTU

Hi everyone, I am using QIIME to analyse my 16S V3-V4 gene illumina dataset.

I have 2 groups of data and each group consists 10 datasets.
I have filtered and combine all 20 set of data and resulting an input file with 3 million of reads.

After I executed against 97_otus.fasta from greengenes.

There is a file 'rep_set.fna' in the output otus directory.
There are over 20k sequence in the rep_set.fna
Only around 300 sequences match with greengenes.
And around 300 otus are New Reference OTU.
Remaining 17k otus are New clean up reference OTU.

Is is normal to have this high no. of denovo OTU?
How should I deal with these denovo OTU? Because they cannot be assigned to any taxonomy in greengenes reference set, what further analyses can be done on them? Thanks!
tsangkl 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 11:04 AM.

Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2018, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO