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The main advantage of RNA-Seq data in this kind of analysis over the microarray platforms is the capability to cover the entire transcriptome, therefore allowing the ...
queryable-rna-seq-database Formally known as the Queryable RNA-Seq Database, this system is designed to simplify the process of RNA-seq analysis by providing the ability upload the result data from RNA-Seq analysis into a database, store it, and query it in many different ways.
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.
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 ...
RNA-Seq experiments generate a large volume of raw sequence reads which have to be processed to yield useful information. Data analysis usually requires a combination of bioinformatics software tools (see also List of RNA-Seq bioinformatics tools) that vary according to the experimental design
It mapped more than 2.2 million reads per CPU hour. That speed allowed the user to process and entire RNA-Seq experiment in less than a day, even on a standard desktop computer. [1] Tophat uses Bowtie in the beginning to analyze the reads, but then does more to analyze the reads that span exon-exon junctions.
The development of high-throughput RNA sequencing (RNA-seq) and microarrays has made gene expression analysis a routine. RNA analysis was previously limited to tracing individual transcripts by Northern blots or quantitative PCR. Higher throughput and speed allow researchers to frequently characterize the expression profiles of populations of ...
Superfast and accurate read aligners. Subread can be used to map both gDNA-seq and RNA-seq reads. Subjunc detects exon-exon junctions and maps RNA-seq reads. They employ a novel mapping paradigm named seed-and-vote. Yes Yes Yes Yes Free, GPL 3 Taipan De-novo assembler for Illumina reads Proprietary, freeware for academic and noncommercial use UGENE