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Related Experiment Videos

Pasha: a versatile R package for piling chromatin HTS data.

Romain Fenouil1, Nicolas Descostes2, Lionel Spinelli3

  • 1Icahn Institute for Genomics and Multiscale Biology, Icahn School of Medicine at Mount Sinai, New York, NY, USA.

Bioinformatics (Oxford, England)
|May 7, 2016
PubMed
Summary

Related Concept Videos

Chromatin Immunoprecipitation- ChIP02:36

Chromatin Immunoprecipitation- ChIP

12.8K
Chromatin immunoprecipitation, or ChIP, is an antibody-based technique used to identify sites on DNA that bind to transcription factors of interest or histone proteins. It also helps determine the type of histone modifications such as acetylation, phosphorylation, or methylation.
Types of ChIP
ChIP can be divided into two types - X-ChIP and N-ChIP. X-ChIP involves in vivo cross-linking of histones and regulatory proteins to DNA, fragmenting the DNA by sonication, and isolating the protein-DNA...
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Pasha is a new R package for processing high-throughput sequencing data. It offers innovative methods for analyzing chromatin-related experiments, improving data manipulation and analysis for ChIP-seq and similar technologies.

Area of Science:

  • Bioinformatics
  • Computational Biology
  • Genomics

Background:

  • High-throughput sequencing (HTS) generates large datasets for biological research.
  • Analyzing chromatin-related HTS data (e.g., ChIP-seq, FAIRE-seq) requires specialized tools.
  • Existing tools may lack specific functionalities for advanced analyses.

Purpose of the Study:

  • To introduce Pasha, an R package for processing aligned reads from chromatin-oriented HTS experiments.
  • To provide users with efficient tools for manipulating and analyzing sequencing data.
  • To offer novel approaches for specific HTS data types.

Main Methods:

  • Development of the Pasha R package.
  • Implementation of read elongation for ChIP-seq data.

Related Experiment Videos

  • Inclusion of a nucleosome midpoint piling strategy for positioning analyses.
  • Functionality for subsetting paired-end reads by insert size groups.

    • Main Results:

    • Pasha facilitates easy manipulation of aligned reads from various short-read sequencing technologies.
    • The package supports innovative analyses like ChIP-seq read elongation and nucleosome positioning.
    • Users can leverage Pasha to extract biologically relevant information from insert size variations.

    Conclusions:

    • Pasha offers a versatile and powerful solution for processing and analyzing chromatin-related HTS data.
    • The package enhances existing analytical capabilities and introduces novel methods.
    • Pasha is a valuable resource for researchers working with ChIP-seq, FAIRE-seq, and MNase-Seq data.