Pipeline Documentation

RNA-Seq pipeline documentation

There are three main folders to seperate scripts out based on where they are written to be run. For a while we will not have replicated scripts in both locations as parts of this process have mostly been run on either Eureka/Cherry-creek or Sysgen/Phenogen but not both and some time will be required to modify the script to run in the other location. Then there are a few scripts that do not need to be run often that are single threads so anywhere with perl or python and the appropriate input files will suffice.

cluster - Mostly specific to running on a cluster(Eureka/Cherry-creek)
singleNode - Mostly specific to running on a single desktop/server may need to adjust the number of processors and watch memory usage.
scripts - Single thread scripts that are less frequently used can probably be run on any environment with perl/python and the input files.

Documentation for Specific Pipelines:

Total RNA
Small RNA