Dataset Information

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

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.

SUBMITTER: Lin J

PROVIDER: S-EPMC6184561 | biostudies-literature | 2018 Oct

REPOSITORIES: biostudies-literature

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

Lin Jiaxing J Gresham Jeremy J Wang Tongrong T Kim So Young SY Alvarez James J Damrauer Jeffrey S JS Floyd Scott S Granek Joshua J Allen Andrew A Chan Cliburn C Xie Jichun J Owzar Kouros K

Bioinformatics (Oxford, England) 20181001 20

<h4>Summary</h4>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-thr ...[more]

PMID: 29790906

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Dataset Information

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

Publications

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

Similar Datasets

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