A Pipeline for Analyzing eCLIP and iCLIP Data with Htseq-clip and DEWSeq.

Individual-nucleotide crosslinking and immunoprecipitation (iCLIP) sequencing and its derivative enhanced CLIP (eCLIP) sequencing are methods for the transcriptome-wide detection of binding sites of RNA-binding proteins (RBPs). This chapter provides a stepwise tutorial for analyzing iCLIP and eCLIP data with replicates and size-matched input (SMI) controls after read alignment using our open-source tools htseq-clip and DEWSeq. This includes the preparation of gene annotation, extraction, and preprocessing of truncation sites and the detection of significantly enriched binding sites using a sliding window based approach suitable for different binding modes of RBPs. © 2022. The Author(s), under exclusive license to Springer Science+Business Media, LLC, part of Springer Nature.

Citation

Sudeep Sahadevan, Thileepan Sekaran, Thomas Schwarzl. A Pipeline for Analyzing eCLIP and iCLIP Data with Htseq-clip and DEWSeq. Methods in molecular biology (Clifton, N.J.). 2022;2404:189-205

PMID: 34694610

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