Benchmarking Scripts Manual

This repository provides scripts to analyze algorithms for determining expressed full length mRNA splice forms from RNA-Seq data.

License

This source code is licensed under the GNU General Public License GPL-2.0.

Obtaining the scripts

To use the code, you can clone the repository to your computer. This will give you the last most stable release.

git clone git://github.com/khayer/benchmarking_scripts.git

If you want to take advantage of the newest changes checkout the develop branch after cloning the repository.

cd benchmarking_scripts
git checkout develop

Testing the code on your system

You can test the code with rake.

cd benchmarking_scripts
rake test

Install

Also you can install the executables with rake.

cd benchmarking_scripts
rake build

Updating

cd benchmarking_scripts
git pull

Format of files

Please see the files in /test/data for an example.

Usage of the executables

stats

Usage: bin/stats CMD file1 file2 [OPTIONS]

CMD
     gff: if file1 is gff format and file2 is geneinfo
     gtf: if file1 is gtf format and file2 is geneinfo
   gfffq: if file1 is gff format and file2 is feature_quant
   gtffq: if file1 is gtf format and file2 is feature_quant
  gffbed: if file1 is gff format and file2 is bed
  gtfbed: if file1 is gtf format and file2 is bed
   bedfq: if file1 is bed format and file2 is feature_quant
  bedbed: if file1 is bed format and file2 is bed
 htseqfq: if file1 is htseq format and file2 is feature_quant

Options
    -l, --log_file LEVEL             Can also be STDOUT or STDERR
    -p, --png_file FILE              Default is fpkm.png
    -f, --fpkm_values FILE           Default is fpkm_values.txt
    -e, --exclude FILE               File with gene names to ignore.
    -a, --annotation FILE            File with annotation given to the algorithm
    -s, --saved_truth FILE           File in marshal format to load
    -t, --print_TP                   Print all TP's?
    -d, --debug                      running in debug mode?
    -h, --help                       help

Example

stats gtffq test/data/test_fq.gtf test/data/test_feature_quant.txt

stats gffbed test/data/test_bed.gff test/data/test.bed