Is it possible to use Maq with the latest version of TopHat? I would like to use Maq to align my reads to a reference genome. Then I would like to use TopHat to call RPKM based on the Maq alignments and a supplied GFF3 file. I think the original version of TopHat used Maq as the alignment program, but the current version used Bowtie. Does anyone know what needs to be done to use the Maq output as the alignment in TopHat?
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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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