ConnectOR (v2.0 - 28/07/2021)

Authors:

• Carlos Pulido (carlos.pulidoquetglas@unil.ch)
• Daniel Kużnicki (dkuznicki@ibch.poznan.pl)

Multiple Species Orthology Finder

Changes in V2:

• Depuration of code
• Simplification and optimization of gene clustering step
• Enhanced summary plot visualization
• Enhanced summary gene sheet

Prerequisites:

• Python3:

  • pickle
  • pandas
  • numpy
  • networkx
  • matplotlib
  • json
  • tqdm

• R:

  • ggplot2
  • gridExtra
  • ggplotify
  • dplyr
  • scales
  • ggrepel

• BedTools

Set Up:

To execute connector clone this repository locally. Following folders/files must be in the same path from command is executed:

• ConnectOR.py
• config
• dictionaries
• ./scripts/

config example (Tab delimited file):

species	assembly_version	annotation	chainmap
Human	hg38	/path/to/human.gtf
Mouse	mm10	/path/to/mouse.gtf
Zebrafish	danRer10	/path/to/zebrafish.gtf

species: name given to each species (must be unique)
assembly_version: ENSEMBL version of the species
annotation [optional]: path to the gtf (recommended to use full path)
chainmap [optional]: comma separated path to each chainmap needed for the analysis (eg for human: "path/to/human_to_mouse.chainmap,path/to/human_to_zebrafish.chainmap"

Execution command:

usage: ConnectOR.v2.py [-h] [-mM MINMATCH] [-g]

ConnectOR (v.2.0) By: Carlos Pulido (carlos.pulido@dbmr.unibe.ch)

optional arguments:

-h, --help show this help message and exit
-mM MINMATCH, --minMatch MINMATCH
       0.N Minimum ratio of bases that must remap in liftOver
       step.Default: 30 (0.30 minimum ratio)
-g, --gene Generate results at gene level along with exon level
       results (default: False)\

Gene Clustering

Orthology - Human (v38) vs Mouse (vM27) - GENCODE

Summary table example:

Gene ID	Species	Biotype	Cluster ID	Cluster Biotype	Cluster type	Gene to hg38	Gene to mm10	Orthologues	in_degree	out_degree
ENSMUSG00000085871.2	mm10	ncRNA	3434	ncRNA	One to one		Predicted	ENSG00000223949.8;ROR1-AS1;ncRNA;chr1:0:64171342:-	1	1
ENSG00000223949.8	hg38	ncRNA	3434	ncRNA	One to one	Predicted		ENSMUSG00000085871.2;Ube2uos;ncRNA;chr4:0:100384998:-	1	1