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