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SpliceMap on Biowulf

SpliceMap is a de novo splice junction discovery and alignment tool. It offers high sensitivity and support for arbitrary RNA-seq read lengths.

SpliceMap is developed by Kin Fau, John Mu and collaborators at the Wong Lab, Stanford University


Programs Location


The easiest way to use the splicemap executables is to add them to your path using the modules commands, as in the example below.
biowulf% module load splicemap      (to add the splicemap executables to your path)

biowulf% module list                (if you want to see what modules you have loaded)
Currently Loaded Modulefiles:
  1) splicemap


Submitting a single batch job

1. Create a script file similar to the one below:

# This file is YourOwnFileName
#PBS -N yourownfilename
#PBS -m be
#PBS -k oe

module load splicemap

cd /data/user/somewhereWithInputFile
runSpliceMap thisrun.cfg
where thisrun.cfg is the file that contains the splicemap configuration options for this run. A sample run.cfg file can be copied from /usr/local/splicemap/run.cfg. A set of sample data is available in /usr/local/splicemap/example.

2. Submit the script using the 'qsub' command on Biowulf.

[user@biowulf]$ qsub -l nodes=1 /data/username/theScriptFileAbove
This command will submit the job to a node with at least 1 GB of memory and 2 cores. If your splicemap run requires more cores, then you may need to submit to a node with larger memory, using a command like
[user@biowulf]$ qsub -l nodes=1:g8 /data/username/theScriptFileAbove

Useful commands:

freen: see

qstat: search for 'qstat' on for it's usage.

jobload: search for 'jobload' on for it's usage.

Submitting a swarm of jobs

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:

module load splicemap; runSpliceMap run1.cfg
module load splicemap; runSpliceMap run2.cfg
module load splicemap; runSpliceMap run3.cfg

Submit this swarm with

biowulf% swarm -f cmdfile

If each splicemap command requires more than 1 GB of memory, then you can specify the required memory per process using the -g # parameter to swarm. e.g. if each splicemap command requires 4 GB of memory:

biowulf% swarm -g 4 -f cmdfile

For more information regarding running swarm, see swarm.html

Running an interactive job

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@biowulf] $ qsub -I -l nodes=1
qsub: waiting for job 2236960.biobos to start
qsub: job 2236960.biobos ready

[user@p4]$ module load splicemap

[user@p4]$ cd /data/userID/splicemap/run1

[user@p4]$ splicemap run1.cfg

[user@p4]  exit
qsub: job 2236960.biobos completed


To allocate an interactive node with a specific amount of memory, use a command like:

[user@biowulf]$ qsub -I -l nodes=1:g24
(to allocate a node with 24 GB of memory)