I am working on amplicon data from an aploid genome (same length, already aligned with a miltiple alignment). Since I cannot generate a .bam file I've to call mutations from aligned fastq through base count generation. To validate a mutation I've to calculate genotype likelihood, but I cannot find a simplified version of the formula, despite I found a 'simpler' formula that expoites counter for GL calculation (https://gwct.github.io/referee/calcs.html). Moreover, all these formulae are not well explained in the page, so I am wondering if someone has already tryed to calculate GL by hand ( having base counts, base qualities and mapping qualities). If possible, I would like to calculate GL in a 'samtools like' manner which is more conservative respect GATK and other tools
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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...-
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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...-
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