Does anyone have any experience with the RPKM (reads per kilobase of exon per million mapped reads) as calculated by TopHat? I can't find any documentation on how this is calculated, and I'm trying to make sure that it standardizes for the total number of mapped reads (as suggested by the name of the metric). I would like to compare RPKM values between samples which have different numbers of total reads and mapped reads, and I'm wondering if I need to do my own standardization for the total number of mapped reads or if this is unnecessary because TopHat has already corrected for it.
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The sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...-
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The field of epigenetics has traditionally concentrated more on DNA and how changes like methylation and phosphorylation of histones impact gene expression and regulation. However, our increased understanding of RNA modifications and their importance in cellular processes has led to a rise in epitranscriptomics research. “Epitranscriptomics brings together the concepts of epigenetics and gene expression,” explained Adrien Leger, PhD, Principal Research Scientist...-
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