SEQanswers

Go Back   SEQanswers > Applications Forums > Metagenomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
Statistical analysis of Centrifuge output MariaF Metagenomics 0 06-27-2018 02:15 AM
g-tubes and centrifuge compatibility JBKri Sample Prep / Library Generation 2 07-02-2015 01:06 AM
Cuffdiff output question jdanderson Bioinformatics 1 10-14-2010 08:13 AM

Reply
 
Thread Tools
Old 01-21-2019, 08:12 AM   #1
pxo289
Junior Member
 
Location: Birmingham UK

Join Date: Mar 2016
Posts: 1
Default Centrifuge output question

Hey,

I've been working with some mouse faecal samples provided to me and was happy enough that they had been classified well by Centrifuge. Then, when I came to actually start using the data I realised I had thousands of classifications which were giving read and unique read counts from single digits to many thousand but an abundance of 0.

I don't know the Expectation-Maximisation algorithm which Centrifuge uses to calculate abundance well enough to know if this is reasonable. To my novice mind it shouldn't matter what model you use if the tool detects the presence of the OTU classified the abundance should never be just 0. Infinitesimally small I could understand, but not a flat nothing.

Any advice on the subject would be appreciated.
pxo289 is offline   Reply With Quote
Reply

Tags
abundance, centrifuge, classification, metagenomics, question

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 11:28 AM.


Powered by vBulletin® Version 3.8.9
Copyright ©2000 - 2019, vBulletin Solutions, Inc.
Single Sign On provided by vBSSO