Alternatively spliced transcript isoforms are commonly observed in higher eukaryotes. The expression levels of these isoforms are key for understanding normal functions in healthy tissues and the progression of disease states. However, accurate quantification of expression at the transcript level ...
Read More »Analysis of EBV Transcription Using High-Throughput RNA Sequencing
High-throughput sequencing of RNA is used to analyze the transcriptomes of viruses and cells, providing information about transcript structure and abundance. A wide array of programs and pipelines has been created to manage and interpret the abundance of data generated ...
Read More »Performance of RNA-seq quantification pipelines is “generally poor”
Obtaining RNA-seq measurements involves a complex data analytical process with a large number of competing algorithms as options. There is much debate about which of these methods provides the best approach. Unfortunately, it is currently difficult to evaluate their performance ...
Read More »ASE-TIGAR – A Bayesian approach for estimating allele-specific expression from RNA-Seq data with diploid genomes
RNA-sequencing (RNA-Seq) has become a popular tool for transcriptome profiling in mammals. However, accurate estimation of allele-specific expression (ASE) based on alignments of reads to the reference genome is challenging, because it contains only one allele on a mosaic haploid ...
Read More »Comparing the normalization methods for the differential analysis of Illumina high-throughput RNA-Seq data
Recently, rapid improvements in technology and decrease in sequencing costs have made RNA-Seq a widely used technique to quantify gene expression levels. Various normalization approaches have been proposed, owing to the importance of normalization in the analysis of RNA-Seq data. ...
Read More »Computational approaches for isoform detection and estimation
The main goal of the whole transcriptome analysis is to correctly identify all expressed transcripts within a specific cell/tissue – at a particular stage and condition – to determine their structures and to measure their abundances. RNA-seq data promise to ...
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