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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
Wolfram Language [6] – the computer language that evolved from the program Mathematica. It has similar statistical capabilities as Mathematica. World Programming System (WPS) – statistical package that supports the use of Python, R and SAS languages within a single user program. XploRe
Python Package Index (formerly the Python Cheese Shop) is the official directory of Python software libraries and modules; Useful Modules in the Python.org wiki; Organizations Using Python – a list of projects that make use of Python; Python.org editors – Multi-platform table of various Python editors
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.
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.
BLAST's nucleotide alignment program, slow and not accurate for short reads, and uses a sequence database (EST, Sanger sequence) rather than a reference genome. BLAT: Made by Jim Kent. Can handle one mismatch in initial alignment step. Yes, client-server Proprietary, freeware for academic and noncommercial use [36] 2002 Bowtie