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SpliceMap on Biowulf & Helix

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.

Sample files can be copied from /usr/local/apps/splicemap/example

Running SpliceMap on Helix

Sample session:

helix$ module load splicemap

helix$ module list

Currently Loaded Modules:
  1) splicemap/3.3.5.2

helix$ cp -r /usr/local/apps/splicemap/example /home/$USER/splicemap

helix$ cd /home/$USER/splicemap/example

helix$ runSpliceMap run.cfg

Running a single batch job on Biowulf

Set up a batch script along the following lines.

#!/bin/bash 

cd /data/$USER/mydir
module load splicemap

runSpliceMap run.cfg

Submit to the batch system with:

$ sbatch myscript

For more memory requirement (default is 4gb), use --mem flag:

$ sbatch --mem=10g myscript

 

Running a swarm of batch jobs on Biowulf

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

cd /data/$USER/mydir1; runSpliceMap run.cfg
cd /data/$USER/mydir2; runSpliceMap run.cfg
cd /data/$USER/mydir3; runSpliceMap run.cfg
[...]   

Submit this job with

$ swarm -f cmdfile --module splicemap

For more memory requirement, use -g flag:

$ swarm -g 10 -f cmdfile --module splicemap

Running an interactive job on Biowulf

Users 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]$ sinteractive 
      salloc.exe: Granted job allocation 1528

[user@pXXXX]$ cd /data/$USER/myruns

[user@pXXXX]$ module load splicemap

[user@pXXXX]$ runSpliceMap run.cfg

[user@pXXXX] exit

[user@biowulf]$ 

Documentation

http://www.stanford.edu/group/wonglab/SpliceMap/