{"id":4806,"date":"2018-07-27T13:21:29","date_gmt":"2018-07-27T13:21:29","guid":{"rendered":"http:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/?page_id=4806"},"modified":"2018-07-27T13:24:22","modified_gmt":"2018-07-27T13:24:22","slug":"marge","status":"publish","type":"page","link":"https:\/\/ri.itservices.manchester.ac.uk\/csf-apps\/software\/applications\/marge\/","title":{"rendered":"Marge"},"content":{"rendered":"

Overview<\/h2>\n

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.<\/p>\n

Version 1.0 for Python3 is installed on the CSF.<\/p>\n

Restrictions on use<\/h2>\n

Please cite your usage of this software as detailed on the MARGE website.<\/p>\n

Set up procedure<\/h2>\n

To access the software you must first load the modulefile:<\/p>\n

module load apps\/gcc\/python-packages\/anaconda3-5.1.0\/marge\/1.0\r\n<\/pre>\n
Running the application<\/h2>\n
Please do not run MARGE on the login node. Jobs should be submitted to the compute nodes via batch.<\/p>\n
A full description of all of the MARGE commands and flags accepted by the application is beyond the scope of this web-page.<\/p>\n
However, you may<\/em> 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:<\/p>\n
marge -h\r\n<\/pre>\n
You must check<\/strong> 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.<\/p>\n
 <\/p>\n
marge init path\/to\/my\/workflow<\/pre>\n
then edit config.json: (the listed tools should now be in your $PATH by loading the modulefile)<\/p>\n
{\r\n\"ASSEMBLY\":\"[hg38|hg19|mm10|mm9]\",\r\n\"MARGEdir\":\"\/usr\/local\/lib\/python3.4\/dist-packages\/marge-1.0-py3.4.egg\/marge\/\",\r\n\"REFdir\":\"\/data\/home\/wangsu\/home2\/MARGE_Pipeline\/MARGE\/reference\",\r\n\"SAMPLESDIR\":\"\/path\/to\/marge_testdata\/\",\r\n\"SAMPLES\":\"sample1 sample2 sample3 sample4(without the suffix .bam)\",\r\n\"EXPSDIR\":\"\/path\/to\/marge_testdata\",\r\n\"EXPS\":\"genelist1 genelist2 genelist3(without the suffix .txt)\",\r\n\"EXPTYPE\":\"[Gene_Only|Gene_Response]\",\r\n\"ID\":\"[GeneSymbol|RefSeq]\",\r\n\"tools\":{\r\n\"MACS2\":\"macs2\",\r\n\"bedClip\":\"bedClip\",\r\n\"bedGraphToBigWig\":\"bedGraphToBigWig\",\r\n\"bigWigAverageOverBed\":\"bigWigAverageOverBed\",\r\n\"bigWigSummary\":\"bigWigSummary\"\r\n}\r\n}\r\n\r\n<\/pre>\n
check with:<\/p>\n
snakemake -n<\/pre>\n
Parallel batch job submission<\/h3>\n
Make sure you have the modulefile loaded then create a batch submission script, for example:<\/p>\n
#!\/bin\/bash\r\n#$ -cwd             # Job will run from the current directory\r\n#$ -V               # Job will inherit current environment settings\r\n#$ -pe smp.pe 8     # Number of cores to use (can be 2 -- 24)\r\n\r\n# $NSLOTS is automatically set to the number of cores specified above\r\nexport OMP_NUM_THREADS=$NSLOTS\r\n\r\n# These commands can be run using multiple cores\r\nsnakemake --cores $NSLOTS\r\n<\/pre>\n
Submit the jobscript using:<\/p>\n
qsub scriptname<\/em><\/pre>\n
where scriptname<\/em> is the name of your jobscript.<\/p>\n
Further info<\/h2>\n