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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.
GT-FAR is an RNA seq pipeline that performs RNA-seq QC, alignment, reference free quantification, and splice variant calling. It filters, trims, and sequentially aligns reads to gene models and predicts and validates new splice junctions after which it quantifies expression for each gene, exon, and known/novel splice junction, and Variant Calling.
TopHat is used to align reads from an RNA-Seq experiment. It is a read-mapping algorithm and it aligns the reads to a reference genome. It is useful because it does not need to rely on known splice sites. [1] TopHat can be used with the Tuxedo pipeline, and is frequently used with Bowtie.
Galaxy [2] is a scientific workflow, data integration, [3] [4] and data and analysis persistence and publishing platform that aims to make computational biology accessible to research scientists that do not have computer programming or systems administration experience.
RNA Seq Experiment. The single-cell RNA-seq technique converts a population of RNAs to a library of cDNA fragments. These fragments are sequenced by high-throughput next generation sequencing techniques and the reads are mapped back to the reference genome, providing a count of the number of reads associated with each gene. [13]
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You are free: to share – to copy, distribute and transmit the work; to remix – to adapt the work; Under the following conditions: attribution – You must give appropriate credit, provide a link to the license, and indicate if changes were made.
Genome assembler can't be directly used in transcriptome assembly for several reasons. First, genome sequencing depth is usually the same across a genome, but the depth of transcripts can vary. Second, both strands are always sequenced in genome sequencing, but RNA-seq can be strand-specific.