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#**piPipes** A set of pipelines developed in the [Zamore Lab](http://www.umassmed.edu/zamore) and [ZLab](http://zlab.umassmed.edu/zlab) to analyze piRNA/transposon from different Next Generation Sequencing libraries (*small RNA-seq*, *RNA-seq*, *Genome-seq*, *ChIP-seq*, *CAGE/Degradome-Seq*). This pipeline provides generic interface for different organisms/genomes with a particular emphasis/optimization on fruitfly ovary and mouse testis samples, which were the main focus in our labs as well as the piRNA field.

Please see the main page for a brief introduction on piPipes and below for detailed description for each tool.

Installation

Small RNA

RNA-seq

CAGE-seq or Degradome-seq

ChIP-seq

Genome-seq

This is the basic directory structure in piPipes

|-- piPipes directory
|   |-- piPipes # main bash script to run
|   |-- piPipes_debug # main bash script to run, debug mode
|   |-- bin # binrary executables
|       |-- smallRNA Seq pipeline
|       |-- Degradome Seq pipeline
|       |-- RNA Seq pipeline
|       |-- CAGE Seq pipeline
|       |-- Genomic Seq pipeline
|       |-- ChIP Seq pipeline
|       |-- binaries like bowtie
|       |-- ...
|   |-- src # source codes
|       |-- bed2_to_bedGraph.cpp # piPipes source codes
|       |-- third_party codes  # source codes of other tools
|       |-- ...
|   |-- common # where annotations and sequences been stored
|       |-- mm9
|       |-- dm3
|           |-- dm3.fa
|           |-- BowtieIndex
|           |-- ...
|       |-- genome_supported.txt # storing the names of genome that has been installed
|       |-- ...