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Hi all, I am currently trying to do some genotyping using some low-pass sequencing data on 13 1000GP samples. I am mostly interested in biallelic SNPS's. I have a variant calling pipeline built on GATK 4 (HaplotypeCaller) using the best practices, and another that uses Varscan2, and another using bcftools/samtools. The idea is to produce two call sets, before and after imputation (with BEAGLE) and check concordance with imputed 1000GP truth sets. Would any of you have suggestions on the best approach here? HaplotypeCaller may not be the best choice if there are only a few or one read is my thought. Any suggestions are appreciated! -Karl
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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 -
Despite advancements in sequencing platforms and related sample preparation technologies, certain sample types continue to present significant challenges that can compromise sequencing results. Pedro Echave, Senior Manager of the Global Business Segment at Revvity, explained that the success of a sequencing experiment ultimately depends on the amount and integrity of the nucleic acid template (RNA or DNA) obtained from a sample. “The better the quality of the nucleic acid isolated...03-22-2024, 06:39 AM