UMMS Affiliation
Department of Biochemistry and Molecular Pharmacology; Program in Bioinformatics and Integrative Biology
Publication Date
2015-02-15
Document Type
Article
Disciplines
Biochemistry, Biophysics, and Structural Biology | Bioinformatics | Computational Biology | Integrative Biology | Systems Biology
Abstract
MOTIVATION: PIWI-interacting RNAs (piRNAs), 23-36 nt small silencing RNAs, repress transposon expression in the metazoan germ line, thereby protecting the genome. Although high-throughput sequencing has made it possible to examine the genome and transcriptome at unprecedented resolution, extracting useful information from gigabytes of sequencing data still requires substantial computational skills. Additionally, researchers may analyze and interpret the same data differently, generating results that are difficult to reconcile. To address these issues, we developed a coordinated set of pipelines, 'piPipes', to analyze piRNA and transposon-derived RNAs from a variety of high-throughput sequencing libraries, including small RNA, RNA, degradome or 7-methyl guanosine cap analysis of gene expression (CAGE), chromatin immunoprecipitation (ChIP) and genomic DNA-seq. piPipes can also produce figures and tables suitable for publication. By facilitating data analysis, piPipes provides an opportunity to standardize computational methods in the piRNA field.
SUPPLEMENTARY INFORMATION: Supplementary information, including flowcharts and example figures for each pipeline, are available at Bioinformatics online.
AVAILABILITY AND IMPLEMENTATION: piPipes is implemented in Bash, C++, Python, Perl and R. piPipes is free, open-source software distributed under the GPLv3 license and is available at http://bowhan.github.io/piPipes/.
CONTACT: Phillip.Zamore@umassmed.edu or Zhiping.Weng@umassmed.edu
SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.
Rights and Permissions
© The Author 2014. Published by Oxford University Press. This is an Open Access article distributed under the terms of the Creative Commons Attribution Non-Commercial License (http://creativecommons.org/licenses/by-nc/4.0/), which permits non-commercial re-use, distribution, and reproduction in any medium, provided the original work is properly cited. For commercial re-use, please contact journals.permissions@oup.com
DOI of Published Version
10.1093/bioinformatics/btu647
Source
Bioinformatics. 2015 Feb 15;31(4):593-5. doi: 10.1093/bioinformatics/btu647. Epub 2014 Oct 17. Link to article on publisher's site
Journal/Book/Conference Title
Bioinformatics (Oxford, England)
Related Resources
PubMed ID
25342065
Repository Citation
Han, Bo W.; Wang, Wei; Zamore, Phillip D.; and Weng, Zhiping, "piPipes: a set of pipelines for piRNA and transposon analysis via small RNA-seq, RNA-seq, degradome- and CAGE-seq, ChIP-seq and genomic DNA sequencing" (2015). Program in Bioinformatics and Integrative Biology Publications and Presentations. 50.
https://escholarship.umassmed.edu/bioinformatics_pubs/50
Creative Commons License
This work is licensed under a Creative Commons Attribution-Noncommercial 4.0 License
Included in
Biochemistry, Biophysics, and Structural Biology Commons, Bioinformatics Commons, Computational Biology Commons, Integrative Biology Commons, Systems Biology Commons