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Marge
Overview
MARGE (Model-based Analysis of Regulation of Gene Expression) is a free software to predict key regulated genes and cis-regulatory regions in human or mouse. A robust methodology that leverages a comprehensive library of genome-wide H3K27ac ChIP-seq profiles to predict key regulated genes and cis-regulatory regions in human or mouse. The framework has three main functions: MARGE-potential, MARGE-express, and MARGE-cistrome.
Version 1.0 for Python3 is installed on the CSF.
Restrictions on use
Please cite your usage of this software as detailed on the MARGE website.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/python-packages/anaconda3-5.1.0/marge/1.0
Running the application
Please do not run MARGE on the login node. Jobs should be submitted to the compute nodes via batch.
A full description of all of the MARGE commands and flags accepted by the application is beyond the scope of this web-page.
However, you may run the following command on the login node to see a list of flag / args that the application will accept. These should be used in your jobscript:
marge -h
You must check whether the command you are using accepts a flag to specify the number of threads (cores) to use. This should then be applied to the command-line in your jobscript.
marge init path/to/my/workflow
then edit config.json: (the listed tools should now be in your $PATH by loading the modulefile)
{
"ASSEMBLY":"[hg38|hg19|mm10|mm9]",
"MARGEdir":"/usr/local/lib/python3.4/dist-packages/marge-1.0-py3.4.egg/marge/",
"REFdir":"/data/home/wangsu/home2/MARGE_Pipeline/MARGE/reference",
"SAMPLESDIR":"/path/to/marge_testdata/",
"SAMPLES":"sample1 sample2 sample3 sample4(without the suffix .bam)",
"EXPSDIR":"/path/to/marge_testdata",
"EXPS":"genelist1 genelist2 genelist3(without the suffix .txt)",
"EXPTYPE":"[Gene_Only|Gene_Response]",
"ID":"[GeneSymbol|RefSeq]",
"tools":{
"MACS2":"macs2",
"bedClip":"bedClip",
"bedGraphToBigWig":"bedGraphToBigWig",
"bigWigAverageOverBed":"bigWigAverageOverBed",
"bigWigSummary":"bigWigSummary"
}
}
check with:
snakemake -n
Parallel batch job submission
Make sure you have the modulefile loaded then create a batch submission script, for example:
#!/bin/bash #$ -cwd # Job will run from the current directory #$ -V # Job will inherit current environment settings #$ -pe smp.pe 8 # Number of cores to use (can be 2 -- 24) # $NSLOTS is automatically set to the number of cores specified above export OMP_NUM_THREADS=$NSLOTS # These commands can be run using multiple cores snakemake --cores $NSLOTS
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.