SpliceMap on 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
Program location
/usr/local/splicemap/bin
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
How To Use
Example
helix% module load splicemap helix% cd /data/user/mydir helix% splicemap run1.cfg
