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
/usr/local/splicemap/binThe 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
1. Create a script file similar to the one below:
#!/bin/bash # This file is YourOwnFileName # #PBS -N yourownfilename #PBS -m be #PBS -k oe module load splicemap cd /data/user/somewhereWithInputFile runSpliceMap thisrun.cfg
2. Submit the script using the 'qsub' command on Biowulf.
[user@biowulf]$ qsub -l nodes=1 /data/username/theScriptFileAbove
[user@biowulf]$ qsub -l nodes=1:g8 /data/username/theScriptFileAbove
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:
module load splicemap; runSpliceMap run1.cfg module load splicemap; runSpliceMap run2.cfg module load splicemap; runSpliceMap run3.cfg [...etc...]
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
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 [user@biowulf]$
To allocate an interactive node with a specific amount of memory, use a command like: