SEQanswers

Go Back   SEQanswers > Applications Forums > Metagenomics



Similar Threads
Thread Thread Starter Forum Replies Last Post
SNPs statistics mmmm Bioinformatics 1 07-28-2014 09:37 PM
Statistics after mapping jomaco Bioinformatics 0 01-26-2012 11:12 AM
454 statistics jordi Bioinformatics 4 01-11-2012 11:10 PM
what statistics and tool to use? vebaev Bioinformatics 16 08-19-2011 12:37 AM
Looking for simple statistics on Roche(454), Illumina & SOLiD platforms Risha Introductions 0 08-29-2010 02:05 PM

Reply
 
Thread Tools
Old 03-31-2018, 11:54 AM   #1
HasanThePupil
Junior Member
 
Location: Virginia

Join Date: Mar 2018
Posts: 1
Smile Simple statistics help

Hello there,

I am currently working on a metagenomics project on the oral microbiome. I am new to metagenomics and not the best at statistics, so please bear with me

I have 3 conditions: a control, an antibiotic-treated, and another type of antibiotic-treated.

I was referred to Metaphlan2, which turned out to be great. Super grateful for the tool. Generated a nice heat map and got some nice preliminary results.

However, I am interested in only extracting bacterial species that have a differential relative abundance of some threshold across treatment groups. What is the easiest way to do this given the output metaphlan2 output (relative abundance)? Any help would be appreciated.
HasanThePupil is offline   Reply With Quote
Old 04-02-2018, 07:28 AM   #2
thermophile
Senior Member
 
Location: CT

Join Date: Apr 2015
Posts: 233
Default

I start with indicator species analysis (indicspecies package in R). you'll need to correct the p-values for multiple comparisons, the package doesn't automatically do that.
__________________
Microbial ecologist, running a sequencing core. I have lots of strong opinions on how to survey communities, pretty sure some are even correct.
thermophile is offline   Reply With Quote
Old 04-04-2018, 01:48 AM   #3
asorbie
Junior Member
 
Location: Munich

Join Date: Jun 2017
Posts: 4
Default

From the same guys that created Metaphlan there's also a tool called LEfSe which you could use for this. It may be easier for you if you're new to this!
asorbie is offline   Reply With Quote
Reply

Tags
metagenomics, metagenomics analysis, relative abundance, statistics

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 09:46 AM.


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