Mcscanx

Introduction

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.

For more information, please check:
Home page: https://github.com/wyp1125/MCScanX A helper command ‘copy_downstream_analyses’ is provided to copy the scripts for downstream analyses. Follow the procedure below to copy the downstream analyses folder to your destination folder: $ copy_downstream_analyses destination_folder

Note

Please follow the recommended citation guidelines from the developers when you use the tool in research.

Versions

Cluster

Version(s)

ANVIL

default

BELL

default

GAUTSCHI

default

NEGISHI

default

SCHOLAR

default

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

Module

You can load the modules by:

module load biocontainers
module load mcscanx

Example job

Warning

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 -p wholenode        # Partition 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
module biocontainers mcscanx

# Your mcscanx workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p cpu         # Partition name
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers mcscanx

# Your mcscanx workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p ai          # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers mcscanx

# Your mcscanx workflow...

#!/bin/bash
#SBATCH -A mygroup     # Group name
#SBATCH -p a100        # Partition name
#SBATCH --gres=gpu:1   # Number of GPUs
#SBATCH --mem=2G       # Memory
#SBATCH -q normal      # QOS name (optional)
#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
module biocontainers mcscanx

# Your mcscanx workflow...

#!/bin/bash
#SBATCH -A queue     # Queue 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
module biocontainers mcscanx

# Your mcscanx workflow...