I am about to commit some serious time to analyzing data produced on a SOLiD 5500 and I had a few questions about sequence quality. First off, does quality matter that much if I have >10 million reads per sample? Second, does quality seriously alter mapping with TOPHAT (RNAseq analysis)? I would think this is less of a problem then if I was doing SNP detection or something. Finally, I can filter the reads with quality scores below 10 easily in GALAXY, but then I lose ~55% of the reads! Seems like a lot. Here are some images pre and post filtering. Am I just trying too hard to clean up the data or should I filter? Thanks in advance.
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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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