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 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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Proteins are often described as the workhorses of the cell, and identifying their sequences is key to understanding their role in biological processes and disease. Currently, the most common technique used to determine protein sequences is mass spectrometry. While still a valuable tool, mass spectrometry faces several limitations and requires a highly experienced scientist familiar with the equipment to operate it. Additionally, other proteomic methods, like affinity assays, are constrained...-
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