ArticleGigaScience2015
Investigation into the annotation of protocol sequencing steps in the sequence read archive.
Article in GigaScience, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 14 papers.
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Who cites it
14 citing papers in PubMed.
- Soft Tissue Ewing Sarcoma Cell Drug Resistance Revisited: A Systems Biology Approach.International journal of environmental research and public health · 2023Article
- A Counterintuitive Neutrophil-Mediated Pattern in COVID-19 Patients Revealed through Transcriptomics Analysis.Viruses · 2022Article
- Microbial Dark Matter: from Discovery to Applications.Genomics, proteomics & bioinformatics · 2022Review
- In Silico Methods for the Identification of Diagnostic and Favorable Prognostic Markers in Acute Myeloid Leukemia.International journal of molecular sciences · 2021Article
- Investigating Molecular Determinants of Cancer Cell Resistance to Ionizing Radiation Through an Integrative Bioinformatics Approach.Frontiers in cell and developmental biology · 2021Article
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- Ten simple rules for annotating sequencing experiments.PLoS computational biology · 2020Article
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- Comprehensive analysis of circRNA expression profiles in humans by RAISE.International journal of oncology · 2017Article
- A Novel Method to Detect Bias in Short Read NGS Data.Journal of integrative bioinformatics · 2017Article
- Calculating the quality of public high-throughput sequencing data to obtain a suitable subset for reanalysis from the Sequence Read Archive.GigaScience · 2017Article
- Article
- Investigation into the annotation of protocol sequencing steps in the sequence read archive.GigaScience · 2015Article
Corrections and comments
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Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundThe workflow for the production of high-throughput sequencing data from nucleic acid samples is complex. There are a series of protocol steps to be followed in the preparation of samples for next-generation sequencing. The quantification of bias in a number of protocol steps, namely DNA fractionation, blunting, phosphorylation, adapter ligation and library enrichment, remains to be determined.
resultsWe examined the experimental metadata of the public repository Sequence Read Archive (SRA) in order to ascertain the level of annotation of important sequencing steps in submissions to the database. Using SQL relational database queries (using the SRAdb SQLite database generated by the Bioconductor consortium) to search for keywords commonly occurring in key preparatory protocol steps partitioned over studies, we found that 7.10%, 5.84% and 7.57% of all records (fragmentation, ligation and enrichment, respectively), had at least one keyword corresponding to one of the three protocol steps. Only 4.06% of all records, partitioned over studies, had keywords for all three steps in the protocol (5.58% of all SRA records).
conclusionsThe current level of annotation in the SRA inhibits systematic studies of bias due to these protocol steps. Downstream from this, meta-analyses and comparative studies based on these data will have a source of bias that cannot be quantified at present.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.