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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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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 -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM