HPC:Sailfish
From HPC wiki
Sailfish
Sailfish is a program intended for Rapid Alignment-free Isoform Quantification from RNA-Seq Reads. Sailfish v0.6.3 is installed on all the PMACS cluster nodes and is made available as an environment module:
[asrini@consign ~]$ bsub -Is bash
[asrini@node061 ~]$ module show sailfish-0.6.3
-------------------------------------------------------------------
/usr/share/Modules/modulefiles/sailfish-0.6.3:
module-whatis Rapid Alignment-free Isoform Quantification from RNA-Seq Reads
prepend-path PATH /opt/software/sailfish/0.6.3/bin
prepend-path LD_LIBRARY_PATH /opt/software/sailfish/0.6.3/lib
-------------------------------------------------------------------
[asrini@node061 ~]$ module load sailfish-0.6.3
[asrini@node061 ~]$ sailfish -h
Allowed Options:
-v [ --version ] print version string
--no-version-check don't check with the server to see if this is the
latest version
-h [ --help ] produce help message
Sailfish v0.6.3
===============
Please invoke sailfish with one of the following commands {index, quant, sf}.
For more inforation on the options for theses particular methods, use the -h
flag along with the method name. For example:
Sailfish index -h
will give you detailed help information about the index command.
