piRNA analysis framework from small RNA-Seq data by a novel cluster prediction tool - PILFER

Genomics. 2018 Nov;110(6):355-365. doi: 10.1016/j.ygeno.2017.12.005. Epub 2017 Dec 19.


With the increasing number of studies focusing on PIWI-interacting RNA (piRNAs), it is now pertinent to develop efficient tools dedicated towards piRNA analysis. We have developed a novel cluster prediction tool called PILFER (PIrna cLuster FindER), which can accurately predict piRNA clusters from small RNA sequencing data. PILFER is an open source, easy to use tool, and can be executed even on a personal computer with minimum resources. It uses a sliding-window mechanism by integrating the expression of the reads along with the spatial information to predict the piRNA clusters. We have additionally defined a piRNA analysis pipeline incorporating PILFER to detect and annotate piRNAs and their clusters from raw small RNA sequencing data and implemented it on publicly available data from healthy germline and somatic tissues. We compared PILFER with other existing piRNA cluster prediction tools and found it to be statistically more accurate and superior in many aspects such as the robustness of PILFER clusters is higher and memory efficiency is more. Overall, PILFER provides a fast and accurate solution to piRNA cluster prediction.

Keywords: Germline; Sequencing read; Small RNA sequencing; Somatic; piRNA; piRNA cluster.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Computational Biology
  • Gene Expression Profiling / methods
  • Humans
  • RNA, Small Interfering*
  • Sequence Analysis, RNA / methods*
  • Software*


  • RNA, Small Interfering