MED Results for "MED-HMP-Example"
A user-friendly interface to make sense of minimum entropy decomposition results.
» 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).
» 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 |
» Files to analyze results further via third partry applications
| Representative sequences per node | node-representatives.fa.txt |
| Read distribution among samples table | read_distribution.txt |
| Sample/oligotype abundance data matrix (percents) | matrix_percents.txt |
| Sample/oligotype abundance data matrix (counts) | matrix_counts.txt |
| Environment file | environment.txt |
| Mapping file | sample_mapping.txt |
| GEXF file for network analysis | network.gexf |
| Basic topology of MED nodes | topology.gexf |
» Total number of reads for each sample that were analyzed.
» Deafult
» cluster_analysis
jaccard |
bray |
kulczynski |
canberra |
horn |
» nmds_analysis
jaccard |
bray |
kulczynski |
canberra |
horn |
» 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
