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

TitlebcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.
Publication TypeJournal Article
Year of Publication2018
AuthorsLin, Jiaxing, Jeremy Gresham, Tongrong Wang, So Young Kim, James Alvarez, Jeffrey S. Damrauer, Scott Floyd, Joshua Granek, Andrew Allen, Cliburn Chan, Jichun Xie, and Kouros Owzar
JournalBioinformatics
Volume34
Issue20
Pagination3581-3583
Date Published2018 10 15
ISSN1367-4811
KeywordsAlgorithms, Clustered Regularly Interspaced Short Palindromic Repeats, Gene Library, High-Throughput Nucleotide Sequencing, RNA, Small Interfering, Software
Abstract

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.

DOI10.1093/bioinformatics/bty402
Alternate JournalBioinformatics
Original PublicationbcSeq: an R package for fast sequence mapping in high-throughput shRNA and CRISPR screens.
PubMed ID29790906
PubMed Central IDPMC6184561
Grant ListP01 CA142538 / CA / NCI NIH HHS / United States
P50 CA190991 / CA / NCI NIH HHS / United States
S10 OD018164 / OD / NIH HHS / United States
Project: