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A research design typically outlines the theories and models underlying a project; the research question(s) of a project; a strategy for gathering data and information; and a strategy for producing answers from the data. [1] A strong research design yields valid answers to research questions while weak designs yield unreliable, imprecise or ...
Whereas high sequence coverage for a genome may indicate the presence of repetitive sequences (and thus be masked), for a transcriptome, they may indicate abundance. In addition, unlike genome sequencing, transcriptome sequencing can be strand-specific, due to the possibility of both sense and antisense transcripts. Finally, it can be difficult ...
The sequencing platform to be used is chosen depending on different factors such as laboratory's research objectives, personal experience and skill levels. So far, the Illumina MiSeq system has proven to be the most commonly used platform for infectious disease research, pathogen surveillance, and pathogen discovery in research and public ...
In medicine, a crossover study or crossover trial is a longitudinal study in which subjects receive a sequence of different treatments (or exposures). While crossover studies can be observational studies, many important crossover studies are controlled experiments, which are discussed in this article.
The use of a sequence of experiments, where the design of each may depend on the results of previous experiments, including the possible decision to stop experimenting, is within the scope of sequential analysis, a field that was pioneered [12] by Abraham Wald in the context of sequential tests of statistical hypotheses. [13]
SOLiD applies sequencing by ligation and dual base encoding. The first SOLiD system was launched in 2007, generating reading lengths of 35bp and 3G data per run. After five upgrades, the 5500xl sequencing system was released in 2010, considerably increasing read length to 85bp, improving accuracy up to 99.99% and producing 30G per 7-day run. [10]
Sequence coverage (or depth) is the number of unique reads that include a given nucleotide in the reconstructed sequence. [1] [2] Deep sequencing refers to the general concept of aiming for high number of unique reads of each region of a sequence. [3] Physical coverage, the cumulative length of reads or read pairs expressed as a multiple of ...
Multiple definitions of the term "batch effect" have been proposed in the literature. Lazar et al. (2013) noted, "Providing a complete and unambiguous definition of the so-called batch effect is a challenging task, especially because its origins and the way it manifests in the data are not completely known or not recorded."