mango: A C++ repository from nsamzhao

Mango

ChIA-PET Analysis Software

Citation

Novel ChIA-PET analysis method reveals two major classes of chromatin interactions Phanstiel DH, Boyle AP, Heidari N, Snyder MP. In Preparation.

Mango Installation

Mango depends on the following R packages.

hash

Rcpp

optparse

They can be installed throug CRAN. For example to install the package 'hash' open R and type the following

install.packages('hash')
install.packages('Rcpp')
install.packages('optparse')

Mango depends on the following software pacakges which should be installed and included in the system PATH prior to using Mango.

Bowtie (http://bowtie-bio.sourceforge.net)

Bedtools (https://github.com/arq5x/bedtools2)

MACS2 (https://github.com/taoliu/MACS)

Once dependencies are installed Mango can be installed from the command line using the following command.

git clone https://github.com/dphansti/mango.git
R CMD INSTALL --no-multiarch --with-keep.source mango

Features

Mango uses fastq files generated by illumina sequencers to call peaks and interactions from ChIA-PET experiments. Arguments can be passed to Mango either by a configuration file, through the command line, or a combination of both. In cases where arguments at supplied both through the command line and a configuration file the values passed via command line arguments will take precidence.

Usage of Mango

Rscript mango.R [-options]

Example for regular interactions calling

Rscript Mango.R --fastq1 samplename_1.fastq --fastq2 samplename_1.fastq --prefix samplename --argfile argfile.txt
   --chromexclude chrM,chrY --stages 1:5

Example of a argfile

bowtieref         = /path/to/hg19
bedtoolsgenome    = /path/to/human.hg19.genome

Parameters

ALL STAGES

stages: stages of the pipeline to execute. stage can be either a single stage (e.g 1 or a range of stagnes e.g 1:5). default = 1:5
prefix: prefix for all output files. default = mango
outdir: The output direcoroy. default = NULL
bowtieref: genome reference file for bowtie
bedtoolsgenome: bedtools genome file
chrominclude: comma separated list of chromosomes to use (e.g. chr1,chr2,chr3,...). Only these chromosomes will be processed. If NULL all chromosomes with be processed. default = NULL
chromexclude: comma separated list of chromosomes to exclude (e.g. chrM,chrY). If NULL all chromosomes with be processed. default = NULL

STAGE 1 PARAMETERS

linkerA: linker sequence to look for. default = GTTGGATAAG
linkerB: linker sequence to look for. default = GTTGGAATGT
minlength: min length of reads after linker trimming. default = 15
maxlength: max length of reads after linker trimming. default = 25
keepempty: Should reads with no linker be kept (TRUE or FALSE). default = FALSE

STAGE 2 PARAMETERS

shortreads: should bowtie alignments be done using paramter for very short reads (~20 bp). default = TRUE

STAGE 4 PARAMETERS

MACS_qvalue: pvalue cutoff for peak calling in MACS2. default = 0.05
MACS_shiftsize: MACS shiftize. NULL allows MACS to determine it
peakslop: Number of basespairs to extend peaks on both sides. default = 500
peakinput: Name of user supplied peaks file. If NULL Mango will use peaks determined from MACS2 analysis. default = NULL
blacklist: BED file of regions to remove from MACS peaks

STAGE 5 PARAMETERS

distcutrangemin: When Mango determines the self-ligation cutoff this is the minimum distance it will consider. default = 1000
distcutrangemax: When Mango determines the self-ligation cutoff this is the maximum distance it will consider. default = 100000
biascut: Mango exlcudes very short distance PETS since they tend to arise from self-ligation of a single DNA framgent as opposed to interligation of two interacting fragments. To determine this distnce cutoff Mango determines the fraction of PETs at each distance that come from self-ligation and sets the cutoff at the point where the fraction is less than or equal to BIASCUT. default = 0.05
FDR: FDR cutoff for significant interactions. default = 0.01
numofbins: number of bins to use for binomial p-value calculations. default = 50
corrMethod: Method to use for correction of mulitply hypothesis testing. See (http://stat.ethz.ch/R-manual/R-devel/library/stats/html/p.adjust.html) for more details. default = BH
maxinteractingdist: The maximum disance (in basepairs) considered for interaction. default = 1000000
extendreads: how many bp to extend reads towards peak. default = 120
FDR: FDR cutoff for interactions. default = 0.01
minPETS: The minimum number of PETs required for an interaction (applied after FDR filtering). default = 2
reportallpairs: Should all pairs be reported or just significant pairs (TRUE or FALSE). default = FALSE

nsamzhao/mango