CADBURE Files

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Comparing Alignment results of user Data Based on the relative reliability and advantage of Uniquely aligned REads

CADBURE is used to evaulate aligner performance on the user data.

Prerequisites
-------------

1. Perl (http://www.perl.org/get.html) (version 5 and above.)
2. Install the two Perl Modules 
      Bio::DB::Sam
      HTML::Table.
2.1. Modules can be easily installed via CPAN as long as CPAN is installed. If CPAN is not installed see here [http://www.cpan.org/modules/INSTALL.html]
     
     #/usr/bin/perl -MCPAN -e 'install Bio::DB::Sam'
Installation of this module requires samtools.
     #/usr/bin/perl -MCPAN -e 'install HTML::Table'

Note: It is recommended to get samtools from Github. Instructions for installing samtools can be found here.
https://github.com/samtools/bcftools/wiki/HOWTOs  

Using the Sample files
----------------------

Usage

       ./CADBURE -f aligner1 -fb Sample_aligner1.bam -s aligner2 -sb Sample_aligner1.bam -o sample-out


Make sure that you have proper permisions to create folder becuase CADBURE creates folders for each Scenarios.

CADBURE outputs summary file in the run directory as a html file with the name you provided to the -o flag. Open the html file using any web-browser. In addition it outputs the read name list associated with the scenarios in the respective folder it creates. For example, output files with the above sample usage will be
       
       Scenario_1/Read-List_Scenario-1_TP_bothAligners.txt
       Scenario_2/Read-List_Scenario-2_FP_aligner1.txt
       Scenario_2/Read-List_Scenario-2_FP_aligner2.txt
       Scenario_3/Read-List_Scenario-3_TP_aligner1.txt
       Scenario_3/Read-List_Scenario-3_TP_aligner2.txt
       Scenario_4/Read-List_Scenario-4_FP_bothAligners.txt
       Scenario_5/Read-List_Scenario-5_FP_aligner1.TN_aligner1.txt
       Scenario_5/Read-List_Scenario-5_FP_aligner2.TN_aligner2.txt
       Scenario_6/Read-List_Scenario-6_TP_aligner1.txt
       Scenario_6/Read-List_Scenario-6_TP_aligner2.txt
       Scenario_7/Read-List_Scenario-7_TN_bothAligners.txt
       Scenario_8/Read-List_Scenario-8_TN_aligner1.txt
       Scenario_8/Read-List_Scenario-8_TN_aligner2.txt

    TP ---> True Positive, FP ---> False Positive, TN ---> True Negative

Statistical Significance on the result
--------------------------------------

To assertain the statistical significance for the difference in both the Specificity and Accuracy of two compared aligners use the provided R code (run_bootstrap_stats.r) like this.

Edit the R script to complete the following two lines and execute the script.

Aligner1.freqs <- c(TP,FP,TN)
Aligner2.freqs <- c(TP,FP,TN)

TP, FP and TN are from the CADBURE ouput for each aligner.

Viewing the Read mappings of the scenarios
------------------------------------------

Open the aligner BAM file in any BAM viewer. We suggest TABLET (http://ics.hutton.ac.uk/tablet/) for its lightweight and high-performance graphical viewer.

We suggest you open two instances of TABLET for viewing the two alignment results. Thereby, you can see the difference in read mapping by the aligners. In the case of sample input files, open 'Sample_aligner1.bam' and 'Sample_aligner1.bam' in two different instances of TABLET. Now open any one of the Scenario folder described above and open the corresponding aligner file to copy a read name. Use the read name to search for mapping in the two different instances of viewer to visualize the difference or similarity.

COPYRIGHT AND LICENSE
---------------------

Copyright 2015-2016 Bioinfolab, Miami Univeristy, Ohio. All Rights Reserved.
Contact: Developer: Praveen K. Raj Kumar [praveenk@pitt.edu] Lab director: Chun Liang [liangc@miamioh.edu]

This program is free software: you can redistribute it and/or modify it under
the terms of the GNU General Public License as published by the Free Software
Foundation, either version 3 of the License, or (at your option) any later
version.

This program is distributed in the hope that it will be useful, but WITHOUT ANY
WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS FOR A
PARTICULAR PURPOSE.  See the GNU General Public License for more details.

You should have received a copy of the GNU General Public License along with
this program.  If not, see <http://www.gnu.org/licenses/>.