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I have been looking at some of my human RNA-Seq data and started to notice some strange things, which brings up some potentially difficult questions. For example do aligners (e.g. tophat) take into account the probability of incorrectly mapping a given 35-bp single end given all the possible derivatives of (0,1,2) mismatches in a given genome? For example, AGG...GCT may be in the genome 100 times more than AAA...AAA? More importantly, given the random placement of reads mapping identically or pseudo-indentically, should we also consider for a given sequence the probability of incorrectly mapping the sequence because there may be 4 places in the genome with ACTG..., but 400 with ATTG... (1bp mismatch) and 4000 with ATTT... (2bp mismatch)?
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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...04-22-2024, 07:01 AM -
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...04-04-2024, 04:25 PM