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The authors who publish an aligner are often required to compare and contrast with existing tools. So you can reads the papers associated with aligners of interest and see if the authors convince you to use their aligner. Of course, the authors have an unavoidable bias towards their own aligner in this scenario.
A number of bloggers have discussed the question informally online. For example:
http://massgenomics.wordpress.com/20...nd-and-others/
Ideally, there would be a paper(s) written by a group that did not have their own aligner that did an objective comparison of many aligners. To be most useful, the comparison would be done with different applications in mind. These applications might have different aligner requirements (e.g. mutation discovery, expression profiling, miRNAs, ChIP-Seq, etc.).
I'm not aware of such a publication right now. Maybe someone else is and will post it. Unfortunately, journal editors (and reviewers) seem notoriously merciless towards such manuscripts ... Anything that fits into a 'platform comparison' category is automatically deemed to be less scientifically valuable, not novel, etc. Indeed some journals explicitly ban submission of this type of work.
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by seqadmin
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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04-22-2024, 07:01 AM -
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by seqadmin
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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