Tximeta: Reference sequence checksums for provenance identification in RNA-seq
Details
Publication Year 2020-02, Volume 16, Issue #2, Page e1007664
Journal Title
PLoS Computational Biology
Publication Type
Journal Article
Abstract
Correct annotation metadata is critical for reproducible and accurate RNA-seq analysis. When files are shared publicly or among collaborators with incorrect or missing annotation metadata, it becomes difficult or impossible to reproduce bioinformatic analyses from raw data. It also makes it more difficult to locate the transcriptomic features, such as transcripts or genes, in their proper genomic context, which is necessary for overlapping expression data with other datasets. We provide a solution in the form of an R/Bioconductor package tximeta that performs numerous annotation and metadata gathering tasks automatically on behalf of users during the import of transcript quantification files. The correct reference transcriptome is identified via a hashed checksum stored in the quantification output, and key transcript databases are downloaded and cached locally. The computational paradigm of automatically adding annotation metadata based on reference sequence checksums can greatly facilitate genomic workflows, by helping to reduce overhead during bioinformatic analyses, preventing costly bioinformatic mistakes, and promoting computational reproducibility. The tximeta package is available at https://bioconductor.org/packages/tximeta.
Publisher
PLOS
WEHI Research Division(s)
Advanced Technology And Biology
PubMed ID
32097405
Open Access at Publisher's Site
https://doi.org/10.1371/journal.pcbi.1007664
Rights Notice
Refer to copyright notice on published article.


Creation Date: 2020-03-24 01:39:42
Last Modified: 2020-03-24 02:17:26
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