piPipes is a coordinated set of pipelines to analyze piRNA (PIWI-interacting RNAs) 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.
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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.
Han BW, Wang W, Zamore PD, Weng Z.
Bioinformatics. 2014 Oct 17. pii: btu647.