MultiRepMacsChIPSeq - Applications

Home

Overview

Usage

Variations

Examples

Applications

Install

Application documentation

Documentation for the applications included in this package.

• annotate_to_tss.pl

  An application to annotate peaks to nearby Transcription Start Sites (TSS, or gene promoters). Unlike most annotation applications, which only report the nearest gene, this reports nearest, left and right proximal, and all neighborhood genes within the given radius.

• bam_partial_dedup.pl

  An application for removing duplicate alignments in a bam file. Unlike other applications, this can sub-sample and remove a random subset of alignments to reach an acceptable fraction of duplication.

• combine_replicate_data.pl

  A simple application to combine the count data of replicates into single sample counts. It works with a tab-delimited text count table file.

• combine_std_chipstats.pl

  An application to combine multiple metric values from Novocraft Novoalign output, bam_partial_dedup duplication statistics, bam2wig shift determination, and Macs2 predictd shift determination.

• generate_differential.pl

  An application to generate a differential track (bedGraph or bigWig format) from two track files.

• generate_mean_bedGraph.pl

  An application to generate chromosomal mean coverage bedGraph from fragment coverage track file.

• intersect_peaks.pl

  An application to properly intersect two or more peak files and generate a merged peak file along with multiple general statistics.

• multirepchipseq.pl

  The main MultiRepMacsChIPSeq pipeline application.

• peak2bed.pl

  An application to convert a narrowPeak file to a simple bed file.

• plot_peak_figures.R

  An R script to generate multiple plot figures from data files generated by the MultiRepMacsChIPSeq pipeline.

• plot_shift_models.R

  An R script to generate a shift model plot from bam2wig shift determination files.

• print_chromosome_lengths.pl

  A simple application to generate a chromosome size file from an indexed track file, such as bam or bigWig.

• recall_peaks.pl

  An application for recalling peaks with different thresholds without having to re-run the entire MultiRepMacsChIPSeq pipeline.

• render.pl

  An application to render a Markdown report into a self-contained HTML file using pandoc, providing reasonable if minimal styling.

• report_mappable_space.pl

  An application to report the fraction of a genome that is covered by unique and non-unique alignments from one or more bam alignment files.

• rmsk2exclusion.pl

  An application to generate empirical exclusion intervals from experimental ChIP, ATAC, or Cut&Run datasets by identifying known repetitive element (RepeatMasker) features with extraordinarily high alignment coverage. This is an alternative approach to identifying empirical exclusion regions when reference or Input data is unavailable.

• run_DESeq2.R

  A simple R script to run DESeq2 on collected peak counts, particularly for differential peak analysis.

• sort_data_by_key.pl

  An application to sort a data table by extrinsic keys, in this case by the samples that contributed to a peak call.

• subset_bigwig.pl

  A convenience utility application to subset one or more bigWig tracks to a single chromosome, ostensibly to download to a personal computer for evaluation in a genome browser.

• update_peak_file.pl

  An application to replace or update missing values in a narrowPeak format peak file using available track files.

Pertinent Bio::ToolBox Applications

• bam2wig.pl

  An application for generating coverage tracks from bam alignment files in nearly every possible way imaginable.

• data2wig.pl

  An application for generating wig, bedGraph, and bigWig files from a tab-delimited text file.

• get_datasets.pl

  An application for collecting data from track files over genomic features in a variety of methods.

• get_relative_data.pl

  An application for collecting data from track files in windows flanking a reference point.

• manipulate_datasets.pl

  An interactive command-line application for working with tab-delimited text data files. Faster and easier than importing into Excel to do simple row- and column-based manipulations.

• manipulate_wig.pl

  An application for performing manipulations on wig, bedGraph, and bigWig file formats.