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The essential parts of that include the program and program version used for the analysis, the method for how the Cq was determined, figuring out the outlier points in the data and how they are used or excluded and why, what results were found for the controls with no template genetic material, an explanation for why the reference genes used ...
fastqp Simple FASTQ quality assessment using Python. Kraken: [9] A set of tools for quality control and analysis of high-throughput sequence data. HTSeq [10] The Python script htseq-qa takes a file with sequencing reads (either raw or aligned reads) and produces a PDF file with useful plots to assess the technical quality of a run.
Hidden Markov model (HMM) and dynamic programming based ab initio gene prediction program [6] DIOGENES Fast detection of coding regions in short genome sequences: Dragon Promoter Finder Program to recognize vertebrate RNA polymerase II promoters: Vertebrates [7] EasyGene
A real-time polymerase chain reaction (real-time PCR, or qPCR when used quantitatively) is a laboratory technique of molecular biology based on the polymerase chain reaction (PCR). It monitors the amplification of a targeted DNA molecule during the PCR (i.e., in real time), not at its end, as in conventional PCR.
Available for R, Python, MATLAB, Julia, and Perl; Primer-E Primer – environmental and ecological specific; PV-WAVE – programming language comprehensive data analysis and visualization with IMSL statistical package; Qlucore Omics Explorer – interactive and visual data analysis software; RapidMiner – machine learning toolbox
If validation of transcript isoforms is required, an inspection of RNA-Seq read alignments should indicate where qPCR primers might be placed for maximum discrimination. The measurement of multiple control genes along with the genes of interest produces a stable reference within a biological context.
Additionally, primer sequences need to be chosen to uniquely select for a region of DNA, avoiding the possibility of hybridization to a similar sequence nearby. A commonly used method for selecting a primer site is BLAST search, whereby all the possible regions to which a primer may bind can be seen. Both the nucleotide sequence as well as the ...
A training data set is a data set of examples used during the learning process and is used to fit the parameters (e.g., weights) of, for example, a classifier. [9] [10]For classification tasks, a supervised learning algorithm looks at the training data set to determine, or learn, the optimal combinations of variables that will generate a good predictive model. [11]