SEQanswers

Go Back   SEQanswers > Bioinformatics > Bioinformatics



Similar Threads
Thread Thread Starter Forum Replies Last Post
clustering based on SNP information strob Bioinformatics 1 07-27-2010 12:04 AM
Efficient frequency-based de novo short-read clustering for error trimming in NGS strob Literature Watch 0 07-02-2009 02:37 AM
PubMed: Efficient frequency-based de novo short read clustering for error trimming in Newsbot! Literature Watch 0 05-15-2009 06:00 AM
SNP Allele-Frequency Determination in Pooled DNA Samples using solexa baohua100 Bioinformatics 1 07-19-2008 01:21 AM

Reply
 
Thread Tools
Old 06-10-2014, 11:23 PM   #1
chayan
Member
 
Location: INDIA

Join Date: Nov 2012
Posts: 46
Default Clustering of samples based on tetra nucleotide frequency

Hi All,

I have assembled several metagenomic samples of various sequencing depth. The contigs have been annotated with COG. Now I want to cluster them based on tetra nucleotide frequency and COG categories.

any suggestions??

thanks
chayan
chayan is offline   Reply With Quote
Old 06-19-2014, 06:48 AM   #2
TiborNagy
Senior Member
 
Location: Budapest

Join Date: Mar 2010
Posts: 329
Default

The frequency of every kmer should be a dimension. Than you can use PCA.
TiborNagy is offline   Reply With Quote
Old 06-20-2014, 12:31 AM   #3
chayan
Member
 
Location: INDIA

Join Date: Nov 2012
Posts: 46
Default

Quote:
Originally Posted by TiborNagy View Post
The frequency of every kmer should be a dimension. Than you can use PCA.
Thanks i did it already but additionaly i want to cluster my samples based on the frequency of cog categories and finaly plot in NMDS (nonmetris mds), as i am not well aware of this so now i am looking for a suitable package
chayan is offline   Reply With Quote
Reply

Tags
bioinformatic tools, cluster identification, k-mer, next gen sequencing, ngs data analysis

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 07:21 AM.


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