bcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.

Journal Article (Journal Article)

SUMMARY: CRISPR-Cas9 and shRNA high-throughput sequencing screens have abundant applications for basic and translational research. Methods and tools for the analysis of these screens must properly account for sequencing error, resolve ambiguous mappings among similar sequences in the barcode library in a statistically principled manner, and be computationally efficient. Herein we present bcSeq, an open source R package that implements a fast and parallelized algorithm for mapping high-throughput sequencing reads to a barcode library while tolerating sequencing error. The algorithm uses a Trie data structure for speed and resolves ambiguous mappings by using a statistical sequencing error model based on Phred scores for each read. AVAILABILITY AND IMPLEMENTATION: The package source code and an accompanying tutorial are available at http://bioconductor.org/packages/bcSeq/. SUPPLEMENTARY INFORMATION: Supplementary data are available at Bioinformatics online.

Full Text

Duke Authors

Cited Authors

  • Lin, J; Gresham, J; Wang, T; Kim, SY; Alvarez, J; Damrauer, JS; Floyd, S; Granek, J; Allen, A; Chan, C; Xie, J; Owzar, K

Published Date

  • October 15, 2018

Published In

Volume / Issue

  • 34 / 20

Start / End Page

  • 3581 - 3583

PubMed ID

  • 29790906

Pubmed Central ID

  • PMC6184561

Electronic International Standard Serial Number (EISSN)

  • 1367-4811

Digital Object Identifier (DOI)

  • 10.1093/bioinformatics/bty402


  • eng

Conference Location

  • England