I'm using TopHat, cufflinks, etc. for the first time and am analyzing two small RNAseq datasets, one of which is derived from a RNAi knockdown of a human gene. I tried looking for the relevant gene in the cuffdiff output to validate the experiment and the analysis. For some reason, the gene is not listed (nor are any genomic loci near it). Problem is, I know there were several reads from this gene in both control and knockdown datasets. Am I misunderstanding how TopHat, cufflinks, etc. work and reports results? To me, it looks like the report should contain all hits regardless of whether a significant difference was found or not.
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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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04-04-2024, 04:25 PM -
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