README.md

aligner_benchmark

Master script

The master script runs both fix_sam.rb and compar2truth.rb for a given aligner.

Usage

    Usage: ruby master.rb [options] run_name dataset source_of_tree

    e.g. run_name = t3r1-test4
    e.g. dataset = t3r1
    e.g. source_of_tree = /project/itmatlab/aligner_benchmark
    
        -a, --algorithm ENUM             Choose from below:
                                         all: DEFAULT
                                         clc
                                         contextmap2
                                         crac
                                         gsnap
                                         hisat
                                         hisat2
                                         mapsplice2
                                         novoalign
                                         olego
                                         rum
                                         star
                                         soapsplice
                                         subread
                                         tophat2
        -d, --debug                      Run in debug mode
        -t, --short                      Only first 1 Million reads
        -s, --species [String]           Spiecies, Default: human
        -v, --verbose                    Run verbosely

On a cluster environment

    bsub ruby master.rb -s malaria t3r3-test t3r3 /project/itmatlab/aligner_benchmark -v

On a specific algorithm

    bsub ruby master.rb -s malaria t3r3-test t3r3  /project/itmatlab/aligner_benchmark -v -a tophat2

Read stats

After master.rb is complete, this code combines the stats of all the given comp_res.txt files.

Usage

    find . -name comp_res.txt |sort | xargs ruby /path/to/read_stats.rb

Anchors

Anchor junction

    ruby anchor_junction.rb /project/itmatlab/aligner_benchmark/statistics/human_t1r1/tophat2/nocoveragesearch-bowtie2sensitive/fixed.sam t1r1 human