MaSC: Mappability-sensitive cross-correlation

Version 1.2.1

A Perl-based reference implementation of Mappability-Sensitive Cross-Correlation (MaSC) for estimating mean fragment length of single-end short-read sequencing data

This software is available free for non-commerical use.

Citation

This repo contains software accompanying the publication "MaSC: Mappability-Sensitive Cross-Correlation to Estimate Fragment Length for Short Read Sequencing Data", Bioinformatics, 2012.

Please cite the above publication if you use the described algorithm or this software.

Description

Given a set of mapped reads and corresponding mappability files, this software provides fragment-length estimation using both naive and mappability-adjusted (MaSC) cross-correlation. Please see the above paper for further details about the methods.

Usage

    MaSC.pl --help --verbose --mappability_path=/mappability/dir/
    --chrom_length_file=/dir/chrom_lens.txt --input_bed=/dir/input.bed
    --prefix=myprefix --smooth_win_size=15 --min_shift=0 --max_shift=400

Options summary

Optional:

Option	Description
--verbose,-h	This switch turns on verbose output, which outputs program status while it is running.
--help,-h	Prints detailed help.
--smooth_win_size,-s	One half of the size of the window to use in the sliding average calculations. For a value of n specified here, the total window size will be 2*n+1. Default is 15.
--min_shift,-min	Minimum shift (d) to calculate. Default is 0.
--max_shift,-max	Maximum shift (d) to calculate. Default is 400.

Required:

Option	Description
--mappability_path,-ma	The directory containing the organism and read-length appropriate mappability wiggle files. These files should indicate only positions where the genome is uniquely mappable. See the example files provided with the test data accompanying this repo. This data can be generated using the UCSC Table Browser, extracting the Mapability track for the genome of interest and filtering for Mapability=1. These file names should be in the form <prefix>_<chromosome_identifier>.map, e.g. hg19_36mer_chr10.map, where the identifiers should match those in CHROMOSOME_LENGTHS_FILE and READ_BED_FILE. Only the chromosomes referenced in MAPPABILITY_DIRECTORY files will be used to calculate the genomic length from the CHROMOSOME_LENGTHS_FILE (option --chrom_length_file, see below).
--chrom_length_file,-ch	A tab-delimited file containing the chromosome lengths. The first column should contain the chromosome identifiers and the second column should contain the corresponding chromosome lengths.
--input_bed,-i	A bed file containing the reads. The chromosomes referenced should correspond to those in the MAPPABILITY_DIRECTORY files.
--prefix,-p	This determines the names of the files that will be output in the directory in which MaSC.pl is run. The software outputs a tab delimited table (_MaSC.txt) and a PNG figure (_MaSC.png) of the naive and MaSC correlation values as a function of shift (d).

Matlab prototype

The software was prototyped in Matlab, which was then formalized in Perl. The Matlab prototype is available in the folder Matlab_prototype.