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I have 11 mpileups generated by novoalign from whole genome sequencing of Daphnia, which has a genome size of ~200MB. Each is the result of alignment of about 130M paired-end illumina reads. I find that all of the mpileups have about 110M lines, implying that we have info for about 55% of the reference. I want to quantify the degree of overlap in coverage among the mpileups. Is there an easy way to do this with samtools or something similar? Also, is there a way to construct an mpileup file that has a line for every site in the reference, rather than just those with read coverage?
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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...Today, 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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