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#piPipes Manual

10-01-2014

piPipes is a set of pipelines developed in the Zamore Lab and ZLab to analyze piRNA/transposon from different Next Generation Sequencing libraries (including small RNA-seq, RNA-seq, Genome-seq, ChIP-seq, CAGE/Degradome-Seq).

Please see the main page for a brief introduction and Wiki pages (https://github.com/bowhan/piPipes/wiki) for detailed description for each pipeline.

piPipes installation and genomes preparation

Small RNA pipeline

RNA-seq pipeline

CAGE-seq/Degradome-seq/RACE pipeline

ChIP-seq pipeline

Genome-seq pipeline

Benchmarks

nomenclature and data formats