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 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...-
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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...-
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04-22-2024, 07:01 AM -
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