Title | Tximeta: Reference sequence checksums for provenance identification in RNA-seq. |
Publication Type | Journal Article |
Year of Publication | 2020 |
Authors | Love, Michael I., Charlotte Soneson, Peter F. Hickey, Lisa K. Johnson, Tessa N Pierce, Lori Shepherd, Martin Morgan, and Rob Patro |
Journal | PLoS Comput Biol |
Volume | 16 |
Issue | 2 |
Pagination | e1007664 |
Date Published | 2020 Feb |
ISSN | 1553-7358 |
Keywords | Algorithms, Animals, Computational Biology, Drosophila melanogaster, Gene Expression Profiling, Genomics, Humans, Mice, Models, Statistical, Pattern Recognition, Automated, Programming Languages, Reproducibility of Results, RNA-Seq, Software, Transcriptome |
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. |
DOI | 10.1371/journal.pcbi.1007664 |
Alternate Journal | PLoS Comput Biol |
Original Publication | Tximeta: Reference sequence checksums for provenance identification in RNA-seq. |
PubMed ID | 32097405 |
PubMed Central ID | PMC7059966 |
Grant List | R01 MH118349 / MH / NIMH NIH HHS / United States R01 HG009937 / HG / NHGRI NIH HHS / United States P01 CA142538 / CA / NCI NIH HHS / United States U41 HG004059 / HG / NHGRI NIH HHS / United States P30 ES010126 / ES / NIEHS NIH HHS / United States |
Tximeta: Reference sequence checksums for provenance identification in RNA-seq.
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