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How much memory should Pindel be using on a 30x whole genome? With the smallest window size it is using a large amount of memory even when the log says it is processing a window with only 1000 reads.
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can you tell me your Pindel version? You could split calculation by 5MB per job. Sometimes there is extreme high coverage at a few small regions. This causes maximum memory usage going high.
Kai -
The version was 0.2.5a4, May 2 2014. We tried using the smallest window (.01) but still maxed out 30Gb of memory.Comment
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Is it possible to send me the log file or console output to my email [email protected]?Originally posted by Nick View PostComment
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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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