title: 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.
abstract: BACKGROUND
  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.
  
  
  BACKGROUND
  Supplementary information, including flowcharts and example figures for each pipeline, are available at Bioinformatics online.
  
  
  METHODS
  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/.
  
  
  BACKGROUND
  Phillip.Zamore@umassmed.edu or Zhiping.Weng@umassmed.edu
  
  
  BACKGROUND
  Supplementary data are available at Bioinformatics online.
authors.affiliation: RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
authors.forename: Bo W
authors.initials: BW
authors.lastname: Han
authors.affiliation: RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
authors.forename: Wei
authors.initials: W
authors.lastname: Wang
authors.affiliation: RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
authors.forename: Phillip D
authors.initials: PD
authors.lastname: Zamore
authors.affiliation: RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA RNA Therapeutics Institute, Howard Hughes Medical Institute, Department of Biochemistry & Molecular Pharmacology and Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, 368 Plantation Street, Worcester, MA 01605, USA.
authors.forename: Zhiping
authors.initials: Z
authors.lastname: Weng
mesh_terms: D000818:Animals; D047369:Chromatin Immunoprecipitation / Q000379:methods*; D019295:Computational Biology / Q000379:methods*; D004251:DNA Transposable Elements / Q000235:genetics*; D029721:Drosophila Proteins / Q000235:genetics; D004331:Drosophila melanogaster / Q000235:genetics; D005260:Female; D005786:Gene Expression Regulation; D016678:Genome; D023281:Genomics / Q000379:methods*; D059014:High-Throughput Nucleotide Sequencing / Q000379:methods*; D010053:Ovary / Q000378:metabolism; D059748:Proteolysis; D012313:RNA / Q000235:genetics; D034741:RNA, Small Interfering / Q000235:genetics*; D017422:Sequence Analysis, DNA / Q000379:methods; D017423:Sequence Analysis, RNA / Q000379:methods; D012984:Software
chemical_list: D004251:DNA Transposable Elements; D029721:Drosophila Proteins; D034741:RNA, Small Interfering; D012313:RNA