gabaldonlab / synthenic-families

Pipeline to classify lncRNA from different species into families according to synthenic relationships.

This pipeline was developed to classify genes from 4 nematode species: C. elegans, C. briggsae, C. remanei and C. brenneri, but it could be easily modified to be used in any other species.

REQUIREMENTS: ftp://ftp.wormbase.org/pub/wormbase/releases/WS248/species/c_elegans/PRJNA13758/annotation/c_elegans.PRJNA13758.WS248.orthologs.txt

1st: for each species, to obtain a file with a sorted list of gene IDs. In this list all chromosomes are concatenated.

#ex:
#WBGene00189949 
#WBGene00021681 
#WBGene00004274 
#XLOC_001892 
#WBGene00199899 
#WBGene00199597 

NOTE: this list can contain all genes in each genome, only protein coding genes, etc.

2nd: to create a file including all orthology relationships for the four nematode species

#usage: python wormbase_orthoParalogsGH.py elegans_genes.list c_elegans.PRJNA13758.WS248.orthologs.txt celegans_ortho.out NOTE: protein coding genes are more prone to have orthology relationships annotated

3rd: to compare gene order between species.The script script produces a file including all lncRNA having conserved syntheny with lncRNA from any of the three other species

#usage: synteny_nematodesv4GH.py sp1_geneOrder.list sp2_geneOrder.list sp3_geneOrder.list sp4_geneOrder.list celegans_ortho.out 4spv4.out cluster overlap minSideGenes noHomology

- cluster (integer): number of genes considered at each side of a given lncRNA; ex: 3. NOTE: if stated 3, the considered size of the cluster is 3+3=6
- overlap (integer): minimum number of shared genes for each pairwise comparisson betwen species; ex: 3
- minSideGenes (integer): minimum number of shared genes at each side of a given lncRNA to be considered as members of the same family; ex: 1
- noHomology (yes/no): yes: to consider genes lacking orthology relationships; no: do not consider genes lacking homology	
ex: python synteny_nematodesv4GH.py celegans_geneOrder.list cbriggsae_geneOrder.list cbrenneri_geneOrder.list cremanei_geneOrder.list celegans_ortho.out out 3 3 1 no

4th: to classify lncRNA from 4 different species into families

#usage: python classifyFamiliesv5_VennGH.py cele cbrig cbren crem 4spv4.out 4spv4_Families.fam 4spv4_Families.txt 4spv4_FAMvenn.R 4spv4_GENESvenn.R >4spv4_Families.counts

- ex INPUT file: 4spv4.out
cele	cbren	XLOC_014828	XLOC_024666
cele	cbren	XLOC_014828	XLOC_024657
- ex INPUT file: cele -> #number of C. elegans genes to classify
- ex INPUT file: cbrig -> #number of C. briggsae genes to classify
- ex INPUT file: cbren -> #number of C. brenneri genes to classify
- ex INPUT file: crem -> #number of C. remanei genes to classify

- ex OUTPUT file: 4spv4_Families.fam
fam1    XLOC_010119cbrig
fam1	XLOC_019544crem
fam1	XLOC_024997cbren
- ex OUTPUT file: 4spv4_Families.txt
	fam1	  bren	brig	 rem
	fam2   	bren   rem
- ex OUTPUT file: 4spv4_Families.counts
	EleBrenBrig 56
	EleBrenRem 51
- ex OUTPUT file: 4spv4_GENESvenn.R -> R script to draw a venn diagram with the number of overlapped genes using R
- ex OUTPUT file: 4spv4_FAMvenn.R -> R script to draw a venn diagram with the number of overlapped families using R