Question: Phylogenetic tree from marker genes
gravatar for David
19 months ago by
David860 wrote:


Trying to give a short resume of what i did:

1 - From a metgenomics illumina 2x150 bp I have cleaned reads and assembled reads into contigs. For each contig i have done gene prediction and extracted bacterial marker genes (based on Campbell et All paper).

2- With bacterial markers genes i have predicted proteins and assigned taxonomy using kaiju (actually diamond or blast will work as well). 

3. So i end up building an abundance table for all my samples (normalized table in RPM).


Now, i would like to compare samples. In 16S i used to work with uifrac distances matrices. The problem here is that i only have the distance matrix so i was wondering what would be the best approach ??

I was thinking of using the ape package a compute a distance matrix of my abudance table but i would like advice.






ADD COMMENTlink written 19 months ago by David860
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.2.0
Traffic: 246 users visited in the last hour