how_are_we_stranded_here: quick determination of RNA-Seq strandedness

Quality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complexity are commonplace, and allow users to implement steps downstream which can account for th...

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Bibliographic Details
Published in:BMC bioinformatics 2022-01, Vol.23 (1), p.49-49, Article 49
Main Authors: Signal, Brandon, Kahlke, Tim
Format: Article
Language:English
Subjects:
Analysis
Archives & records
Bioinformatics
Computational biology
Contamination
Gene expression
Gene sequencing
Genomes
High-Throughput Nucleotide Sequencing
Layouts
Methods
Quality control
Reproducibility of Results
Ribonucleic acid
RNA
RNA sequencing
RNA-Seq
Sequence analysis
Sequence Analysis, DNA
Sequence Analysis, RNA
Software
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Summary:Quality control checks are the first step in RNA-Sequencing analysis, which enable the identification of common issues that occur in the sequenced reads. Checks for sequence quality, contamination, and complexity are commonplace, and allow users to implement steps downstream which can account for these issues. Strand-specificity of reads is frequently overlooked and is often unavailable even in published data, yet when unknown or incorrectly specified can have detrimental effects on the reproducibility and accuracy of downstream analyses. To address these issues, we developed how_are_we_stranded_here, a Python library that helps to quickly infer strandedness of paired-end RNA-Sequencing data. Testing on both simulated and real RNA-Sequencing reads showed that it correctly measures strandedness, and measures outside the normal range may indicate sample contamination. how_are_we_stranded_here is fast and user friendly, making it easy to implement in quality control pipelines prior to analysing RNA-Sequencing data. how_are_we_stranded_here is freely available at https://github.com/betsig/how_are_we_stranded_here .
ISSN:1471-2105
1471-2105
DOI:10.1186/s12859-022-04572-7