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Bart
Overview
Bart (Binding Analysis for Regulation of Transcription) is a bioinformatics tool for predicting functional transcription factors (TFs) that bind at genomic cis-regulatory regions to regulate gene expression in the human or mouse genomes, given a query gene set or a ChIP-seq dataset as input. BART leverages 3,485 human TF binding profiles and 3,055 mouse TF binding profiles from the public domain (collected in Cistrome Data Browser) to make the prediction.i
Version 1.0.1 for Python3 is installed on the CSF.
Restrictions on use
There are no restrictions on accessing the software on the CSF. It is released under the BSD 2-Clause “Simplified” License and all usage must adhere to that license.
Please cite your usage of this software as detailed on the BART website.
Set up procedure
To access the software you must first load the modulefile:
module load apps/gcc/python-packages/anaconda3-5.1.0/bart/1.0.1
Running the application
Please do not run BART on the login node. Jobs should be submitted to the compute nodes via batch.
A full description of all of the BART 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:
bart -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.
Serial 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 # These commands will only use one core bart geneset -i ../RandoGenes.txt -s mm10 --outdir ./Bart_test -p 1 -t ../target.txt
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
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 bart geneset -i ../RandoGenes.txt -s mm10 --outdir ./Bart_test -p $NSLOTS -t ../target.txt
Submit the jobscript using:
qsub scriptname
where scriptname is the name of your jobscript.
Further info
Updates
None.