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#**Piper** This is an integrated pipeline 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 (*small RNA-Seq, RNA-Seq, Genomic-Seq, ChIP-Seq, CAGE-Seq and Degradome-Seq*). This pipeline provides generic interface for different organisms/genomes with a particular emphasis/optimization on fruit-fly 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 piper and below for detailed description for each tool.

installation

smallRNA

RNASeq

CAGESeq or DegradomeSeq

GenomeSeq

ChIPSeq

This is the basic directory structure in pipie

|-- piper directory
|   |-- piper # main bash script to run
|   |-- 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 # piper 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
|       |-- ...