| Literature DB >> 30710114 |
Binbin Wang1, Mei Wang2, Wubing Zhang1, Tengfei Xiao3,4, Chen-Hao Chen3, Alexander Wu3,5, Feizhen Wu6,7, Nicole Traugh3, Xiaoqing Wang3, Ziyi Li1, Shenglin Mei1, Yingbo Cui8, Sailing Shi1, Jesse Jonathan Lipp9, Matthias Hinterndorfer9, Johannes Zuber9, Myles Brown3,10, Wei Li11,12, X Shirley Liu13,14.
Abstract
Genome-wide screening using CRISPR coupled with nuclease Cas9 (CRISPR-Cas9) is a powerful technology for the systematic evaluation of gene function. Statistically principled analysis is needed for the accurate identification of gene hits and associated pathways. Here, we describe how to perform computational analysis of CRISPR screens using the MAGeCKFlute pipeline. MAGeCKFlute combines the MAGeCK and MAGeCK-VISPR algorithms and incorporates additional downstream analysis functionalities. MAGeCKFlute is distinguished from other currently available tools by its comprehensive pipeline, which contains a series of functions for analyzing CRISPR screen data. This protocol explains how to use MAGeCKFlute to perform quality control (QC), normalization, batch effect removal, copy-number bias correction, gene hit identification and downstream functional enrichment analysis for CRISPR screens. We also describe gene identification and data analysis in CRISPR screens involving drug treatment. Completing the entire MAGeCKFlute pipeline requires ~3 h on a desktop computer running Linux or Mac OS with R support.Entities:
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Year: 2019 PMID： 30710114 PMCID： PMC6862721 DOI： 10.1038/s41596-018-0113-7
Source DB: PubMed Journal: Nat Protoc ISSN： 1750-2799 Impact factor: 13.491