HPC:Sailfish

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.

Other Pages

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• HPC FAQ
• Connecting to the PMACS cluster
• User Guide
• Available Software
• PMACS Archive System