Pseudogene pipeline

Scripts and wrapper file for runing the Shiu Lab's pseduogene pipeline.

Overview

Requirements

• python (2.7 or later, not 3; https://www.python.org/downloads/)
• python scripts in the _pipeline_scripts folder
• RepeatMaster (http://www.repeatmasker.org/)
• tfasty (part of the FASTA package, version 36 or later; http://faculty.virginia.edu/wrpearson/fasta/)

Useage

The pipline is run using:

 _wrapper_scripts/CombinedPseudoWrapper.py [parameter_file]

An example parameter_file can found in in the _example_files folder

Additionally, a test case using chromosome 4 from A. thaliana can be run from the _testcase folder using the following command from within _testcase. You will need to supply the path to your local FASTA install and the name of the tfasty program you are using in test_parameter_file.txt.

 python ../_wrapper_scripts/CombinedPseudoWrapper.py test_parameter_file.txt

The test case takes about 15-30 minutes to run. Expected results of this run can be found in the _expected_results subfolder

Ouput

The output of the pipeline is seperated into the following subfolder:

• _intermediate: Intermediate files used to generate final results.
  • These may be removed following a successful run, however if you want a list of pseudogenes generated prior to high confidence filtering and/or RepatMasker filtering they will be here
• _logs: log files generated by the run
• _results: Output files for the final list of pseudogenes following high confidence and and RepeatMasker filtering
  1. hiConf.RMfilt/hiConf.RMfilt.cdnm - position information for pseudogenes
  2. fa.hiConf.RMfilt/fa.hiConf.RMfilt.cdnm - sequence information for pseudogenes
  3. hiConf.RMfilt.cdnm.gff - gff file with pseudogene annotations
  • NOTE: cdnm versions of the output use simplified pseudogene names.