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I am currently working on trying to obtain the general statistics on a set of SNPs. I have the original vcf file that I used in Plink to analyze for LD, HWE, etc. I now have a filtered set of SNPs I would like to run through snpEff. Unfortunately, even when I use PGDspider to convert the .ped and .map file back into a .vcf, I have lost the original chromosome names from the original .vcf file as the chromosome ids get changed in the process .vcf to .ped. I need the chromosome id to be the original id so it will correspond to the reference genome in snpEff. Does anyone have any ideas on how to do this? Any help will be appreciated!
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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 on Modified Bases...Today, 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