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The biobambam package contains a tool called bammarkduplicates. It produces results which should be quite similar to those of Picard's MarkDuplicates tool while avoiding the sometimes high memory requirements of the Java implementation. The source code is available on github at https://github.com/gt1/biobambam, binaries for some versions of Linux are at ftp://ftp.sanger.ac.uk/pub/users/gt1/biobambam and also on launchpad https://launchpad.net/biobambam . It was developed at the Sanger Institute because the Java tool failed with out of memory type errors for a number of (at least locally high depth) BAM files, which required manual intervention (rerunning compute jobs with higher memory settings, which blocks otherwise free CPU cores because a single one is using all the RAM). If someone is interested in the algorithmic background, there is a preprint at http://arxiv.org/abs/1306.0836 .
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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
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