MultiRepMacsChIPSeq - Applications

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Applications

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Application documentation

Documentation for the applications included in this package.

• 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.

• multirep_macs2_pipeline.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.

• 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.