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DESeq2 is a software package in the field of bioinformatics and computational biology for the statistical programming language R.It is primarily employed for the analysis of high-throughput RNA sequencing (RNA-seq) data to identify differentially expressed genes between different experimental conditions.
PathwaySeq [154] Pathway analysis for RNA-Seq data using a score-based approach. petal Co-expression network modelling in R. ToPASeq: [155] an R package for topology-based pathway analysis of microarray and RNA-Seq data. RNA-Enrich A cut-off free functional enrichment testing method for RNA-seq with improved detection power.
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RNA-Seq (named as an abbreviation of RNA sequencing) is a technique that uses next-generation sequencing to reveal the presence and quantity of RNA molecules in a biological sample, providing a snapshot of gene expression in the sample, also known as transcriptome. [2] [3]
It is the first step in sequence analysis to limit wrong conclusions due to poor quality data. The tools used at this stage depend on the sequencing platform. For instance, FastQC checks the quality of short reads (including RNA sequences), Nanoplot or PycoQC are used for long read sequences (e.g. Nanopore sequence reads), and MultiQC ...
Visualize next generation sequencing data (BAM files) using UGENE Assembly Browser; Variant calling with SAMtools [8] RNA-Seq data analysis with Tuxedo pipeline (TopHat, [9] Cufflinks, [10] etc.) ChIP-seq data analysis with Cistrome pipeline (MACS, [11] CEAS, [12] etc.) Raw NGS data processing; HMMER 2 and 3 packages integration; Chromatogram ...
Illumina sequencing: it offers a good method for small RNA sequencing and it is the most widely used approach. [7] After the library preparation and amplification steps, the sequencing (based on the use of reversible dye-terminators ) can be performed by using different systems, such as Miseq System, Miseq Series, NextSeq Series and many others ...
For a pure RNA sample, the A 230:260:280 should be around 1:2:1, and for a pure DNA sample, the A 230:260:280 should be around 1:1.8:1. [9] Absorption at 330 nm and higher indicates particulates contaminating the solution, causing scattering of light in the visible range. The value in a pure nucleic acid sample should be zero. [citation needed]