RefGen

User Manual for RefGen version 1.0

CONTENTS OF THIS FILE

• Introduction
• Requirements
• Installation
• Usage
• Troubleshooting
• Maintainers

INTRODUCTION

Given a set of experiments this algorithm takes as input a list of genomic intervals, and it returns a reference defined by the genomic positions which are spanned by more than τ intervals. RefGen first exploits the lists of genomic intervals to generate a genomic coverage (i.e. the overlapping value among intervals), then the genomic position characterized by a coverage value greater than or equal to a selected threshold τ are selected as reference.

The use of the τ threshold makes the overlap of multiple experiments independent of the length and the number of genomic regions belonging to the input datasets. Since the τ value reflects the number of experiments in which the genomic regions have to be identify, the selection of a specific τ value is related to the level of the severity chosen for the analysis.

For details of this analysis see:

Ferrero, G., Miano, V., Beccuti, M., Balbo, G., De Bortoli, M., & Cordero, F. (2017). Dissecting the genomic activity of a transcriptional regulator by the integrative analysis of omics data. Scientific reports, 7(1), 8564.

Please cite this paper when using this code.

REQUIREMENTS

• C++
• Perl (optional, for identification of multiple genomic intervals)

INSTALLATION

• You may use RefGen algorithm by directly run the 64-bit binary file (no compilation is needed), or you may build it from the source. For build the program from source type "make" in the installation folder.

USAGE

• For RefGen usage on a specific genomic interval:

  RefGen <input_file> <output_file> <lower_bound> <upper_bound>

   - input_file = Name of the input file;
   - output_file = Name of the output file;
   - lower_bound = Starting position of the genomic region of interest (in 0-based system);
   - upper_bound = End position of the genomic region of interest (in 0-based system);
   - threshold = τ threshold representing the minimum number of genomic intervals that have to be overlapped to define an output interval;
   - Chromosome = Chromosome identifier.
  

• For an automatic application of RefGen on multiple genomic intervals:

  perl Run.pl <input_file>

   - input_file = The folder which collects the input datasets;
   - chrs = Tab-separated file reporting the name and the lenght of the chromosome analysed. Chromosome length for human genome hg18, hg19 and hg38 are
   		 provided in the Chromosome_sizes folder;
   - threshold = τ threshold representing the minimum number of genomic regions reporting overlapped within the genomic region of interest.
  

• Example of single chromosome (chr1) analysis to identify intervals observed in all the 3 experiment replicates:

   cat ./Input_example/*.bed > ./Input_example/Input_merged.bed
   
   ./RefGen ./Input_example/Input_merged.bed ./Input_example/Overlapped_regions_chr1.bed 0 249250621 3 chr1
  

• Example of multiple chromosome analysis:

   cat ./Input_example/*.bed > ./Input_example/Input_merged.bed
  
   perl Run.pl ./Input_example/Input_merged.bed ./Chromosome_sizes/hg19.chrom.sizes.txt 3
  

MAINTAINERS

• Beccuti Marco (University of Turin) - http://www.di.unito.it/~beccuti/
• Ferrero Giulio (University of Turin) - http://www.di.unito.it/~ferrero/

/***************************************************************************

• Copyright (C) 2016 by Marco Beccuti and Giulio Ferrero *
• [email protected] *

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• This program is free software; you can redistribute it and/or modify *
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• This program is distributed in the hope that it will be useful, *
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• MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the *
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