RNASeqCommandLine

Introduction

To run AltAnalyze from command-line, you will need to have installed AltAnalyze and make sure the source code is in the AltAnalyze program main directory. If you have downloaded the python-source code or Linux version, this will be the case, otherwise, you will need to copy the contents of the folder "Source_code" to the parent AltAnalyze directory. Before supplying the command-line argument to this program, you will need to open a command prompt and change to the directory with the AltAnalyze source code.

Examples:

Downloading and installing a species specific database (human)

python AltAnalyze.py --species Hs --update Official --version EnsMart65

Exporting a Exon BED reference file for BedTools

python AltAnalyze.py --species Hs --platform RNASeq --bedDir "C:/BEDFiles"
  --output "C:/BEDFiles" --expname "hESC_differentiation" --buildExonExportFile yes

Analyzing BED files – RNASeq Junction Bed files using default options

python AltAnalyze.py --species Hs --platform RNASeq --bedDir "C:/BEDFiles"
  --groupdir "C:/BEDFiles/groups.hESC_differentiation.txt"
  --compdir "C:/BEDFiles/comps.hESC_differentiation.txt" --output "C:/BEDFiles"
  --expname "hESC_differentiation"

Analyzing BED files – RNASeq Junction Bed files using custom options

Note: before running the below command, you will need to have created and saved the groups and comps files to the ExpressionInput directory. See here for instructions.

python AltAnalyze.py --species Hs --platform RNASeq --bedDir "C:/BEDFiles"
  --groupdir "C:/BEDFiles/ExpressionInput/groups.hESC_differentiation.txt"
  --compdir "C:/BEDFiles/ExpressionInput/comps.hESC_differentiation.txt"
  --output "C:/BEDFiles" --expname "hESC_differentiation"

For details on how to format generate and format the input text files, go here.