FusionMap is an efficient fusion aligner which aligns reads spanning fusion junctions directly to the genome without prior knowledge of potential fusion regions. It detects and characterizes fusion junctions at base-pair resolution. FusionMap can be applied to detect fusion junctions in both single- and paired-end dataset from either gDNA-Seq or RNA-Seq studies.

/usr/local/fusionmap/bin

The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands, 'module load fusionmap' , as in the example below.

Frequently used module commands:

$ module load AppName
$ module load AppName/AppVersion
$ module unload AppName
$ module avail
$ module avail AppName
$ module list
$ module switch AppName AppName/AppVersion
$ module display AppName

For bash users:

export PATH=/usr/local/fusionmap/bin:/usr/local/mono/bin:$PATH

For tcsh/csh users:

set path=(/usr/local/fusionmap/bin /usr/local/mono/bin ${path})

1. Create a script file. The file will contain the lines similar to the lines below. Modify the path of program location before running.

#!/bin/bash
# This file is YourOwnFileName
#
#PBS -N yourownfilename
#PBS -m be
#PBS -k oe

module load fusionmap
cd /data/user/somewhereWithInputFile
fusionmap command 1
fusionmap command 2
....
....

2. Submit the script using the 'qsub' command on Biowulf, e.g. Note, user is recommend to run benchmarks to determine what kind of node is suitable for his/her jobs.

Useful commands:

freen: see http://biowulf.nih.gov/user_guide.html#freen

qstat: search for 'qstat' on http://biowulf.nih.gov/user_guide.html for it's usage.

jobload: search for 'jobload' on http://biowulf.nih.gov/user_guide.html for it's usage.

Using the 'swarm' utility, one can submit many jobs to the cluster to run concurrently.

Set up a swarm command file (eg /data/username/cmdfile). Here is a sample file:

There are one flag of swarm that's required '-f' and two other flags of swarm user most possibly needs to specify when submit a swarm job: '-t' and '-g'.

-f: the swarm command file name above (required)
-t: number of processors per node to use for each line of the commands in the swarm file above.(optional)
-g: GB of memory needed for each line of the commands in the swarm file above.(optional)

By default, each line of the commands above will be executed on '1' processor core of a node and uses 1GB of memory. If this is not what you want, you will need to specify '-t' and '-g' flags when you submit the job on biowulf.

Say if each line of the commands above also will need to use 10gb of memory instead of the default 1gb of memory, make sure swarm understands this by including '-g 10' flag:

[user@biowulf]$ swarm -g 10 -f cmdfile

For more information regarding running swarm, see swarm.html

User may need to run jobs interactively sometimes. Such jobs should not be run on the Biowulf login node. Instead allocate an interactive node as described below, and run the interactive job there.

User may add property of node in the qsub command to request specific interactive node. For example, if you need a node with 24gb of memory to run job interactively, do this:

http://www.omicsoft.com/fusionmap/