I have illumina RNASeq data for of 3 samples each with untreated and treated conditions. Thus i have three biological replicates for each conditions. I am not expecting much change after the 'treatment'; What parameters of DESeq and Cuffdiff do I need to tweak to handle conditions with more 'similarity' than 'difference' ? what normalization method should be used in cuffdiff2 , the default geometric mean normalisation, upper quartile normalisation (-N) or --raw-mapped-norm ?
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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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