mcscanx
The MCScanX package has two major components: a modified version of MCscan algorithm allowing users to handle MCScan more conveniently and to view multiple alignment of syntenic blocks more clearly, and a variety of downstream analysis tools to conduct different biological analyses based on the synteny data generated by the modified MCScan algorithm.
Home page: https://github.com/wyp1125/MCScanX.
Link to section 'Versions' of 'mcscanx' Versions
- default
Link to section 'Commands' of 'mcscanx' Commands
- MCScanX
- MCScanX_h
- duplicate_gene_classifier
- add_ka_and_ks_to_collinearity
- add_kaks_to_synteny
- detect_collinearity_within_gene_families
- detect_synteny_within_gene_families
- group_collinear_genes
- group_syntenic_genes
- origin_enrichment_analysis
Link to section 'Introduction' of 'mcscanx' Introduction
Link to section 'Module' of 'mcscanx' Module
You can load the modules by:
module load biocontainers
module load mcscanx
Helper command
To conduct downstream analyses, users need to copy the folder downstream_analyses from container into the host system.
A helper command copy_downstream_analyses is provided to simplify the task. Follow the procedure below to copy downstream_analyses into target directory:
$ copy_downstream_analyses $PWD # this will copy the downstream_analyses into the current directory.
Link to section 'Example job' of 'mcscanx' Example job
Using #!/bin/sh -l as shebang in the slurm job script will cause the failure of some biocontainer modules. Please use #!/bin/bash instead.
To run mcscanx on our clusters:
#!/bin/bash
#SBATCH -A myallocation # Allocation name
#SBATCH -t 1:00:00
#SBATCH -N 1
#SBATCH -n 1
#SBATCH --job-name=mcscanx
#SBATCH --mail-type=FAIL,BEGIN,END
#SBATCH --error=%x-%J-%u.err
#SBATCH --output=%x-%J-%u.out
module --force purge
ml biocontainers mcscanx
## Run MCScanX
MCScanX Result/merge
## Copy downstream_analyses
copy_downstream_analyses $PWD
## Downstream analyses
java circle_plotter -g ../Result/merge.gff -s ../Result/merge.collinearity -c ../Result/merge_circ.ctl -o ../Result/merge_circle.png
java dot_plotter -g ../Result/merge.gff -s ../Result/merge.collinearity -c ../Result/merge_dot.ctl -o ../Result/merge_dot.png
java dual_synteny_plotter -g ../Result/merge.gff -s ../Result/merge.collinearity -c ../Result/merge_dot.ctl -o ../Result/merge_dual_synteny.png