MED Results for "MED-HMP-Example"
A user-friendly interface to make sense of minimum entropy decomposition results.
Overview

» A summary of what happened.

Minimum Entropy Decomposition analysis was performed on 178,461 read from 18 samples for "MED-HMP-Example" with MED pipeline version 0.1-alpha (available from http://oligotyping.org/MED).

General Information

» Meta

Library version 0.1-alpha
 
Run date 11 Jul 14 17:40:04
End of run 11 Jul 14 17:47:33

» Given Parameters

Min entropy for a component to be picked for decomposition 0.0965
Perform entropy normalization heuristics True
Max number of discriminants to use for decomposition 4
Min total abundance of oligotype in all samples 0
Min substantive abundance of an oligotype (-M) 15
Maximum variation allowed in each node (-V) 4 nt
Nodes agglomerated based on co-occurence patterns
Merge homopolymer splits False
Skip removing outliers False
Try to relocate outliers False

» Input Data

Number of sequences analyzed 178,461
Number of samples found 18
Number of characters in each alignment 935
Average read length (without gaps) 415

» Handling Outliers

 
Outliers removed due to -M 19,701
Outliers removed due to -V 5,862
Total number of outliers removed during the refinement 25,563
 
Relocated outliers originally removed due to -M
Relocated outliers originally removed due to -V
Total number of relocated outliers
 
Final number of outliers due to -M 19,701
Final number of outliers due to -V 5,862
Final total number of outliers 25,563

» Nodes

Number of sequences analyzed 178,461
Number of sequences represented after quality filtering 152,898
Number of raw nodes (before the refinement) 388
Number of final nodes (after the refinement) 388
Downloads

» Files to analyze results further via third partry applications

Representative sequences per nodenode-representatives.fa.txt
Read distribution among samples tableread_distribution.txt
Sample/oligotype abundance data matrix (percents)matrix_percents.txt
Sample/oligotype abundance data matrix (counts)matrix_counts.txt
Environment fileenvironment.txt
Mapping filesample_mapping.txt
GEXF file for network analysisnetwork.gexf
Basic topology of MED nodestopology.gexf
Read Distribution per Sample

» Total number of reads for each sample that were analyzed.

Basic Analyses

» Deafult

» cluster_analysis

jaccard

bray

kulczynski

canberra

horn

» nmds_analysis

jaccard

bray

kulczynski

canberra

horn

Exclusive Analyses

» another

» nmds_analysis

jaccard

bray

kulczynski

canberra

horn

» heatmap_analysis

jaccard

bray

kulczynski

canberra

horn

» something

» nmds_analysis

jaccard

bray

kulczynski

canberra

horn

» heatmap_analysis

jaccard

bray

kulczynski

canberra

horn

» groups

» nmds_analysis

jaccard

bray

kulczynski

canberra

horn

» heatmap_analysis

jaccard

bray

kulczynski

canberra

horn