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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.
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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 sequencing world is rapidly changing due to declining costs, enhanced accuracies, and the advent of newer, cutting-edge instruments. Equally important to these developments are improvements in sequencing analysis, a process that converts vast amounts of raw data into a comprehensible and meaningful form. This complex task requires expertise and the right analysis tools. In this article, we highlight the progress and innovation in sequencing analysis by reviewing several of the...Yesterday, 07:48 AM -
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
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