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I am using Unified Genotyper for SNP calling. I find that the reported Allele depths and read depths seem much lower than expected (with and without the base quality recalibration). I did the alignment using CLC bio and have a SNP file from CLC bio which reports the coverage at the SNP position of reads that passed the quality filter. I understand the reported coverage values may not be exact but for equivalent quality scores, I find the DP from GATK to be 10% or 20% of the CLC bio coverage. Has anyone else seen this? Does GATK scale down the coverage?
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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...Yesterday, 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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