Hey, anyone here experienced with HTSJDK?
I'm currently using it to read VCF files (bi-allelic microarray derived) and grab all the genotypes for all the individuals then transform them into a Byte Array, storing each genotype as the sum of it's indices (so ./. > -2, 0/0 > 0, 0/1 > 1, 1/1 > 2 etc). Using other language (cyvcf2 etc) libraries they often natively provide genotypes as indices. However, with HTSJDK when requesting genotypes from a VariantContext with getGenotypes() you get the genotypes in base form (something like [A*, C], [A*, A*], [C, C] where each allele is it's own object). Currently I'm using getAlleleIndices() from VariantContext to convert these Genotype objects back into an Array of indices which I can then sum. This is a bit slower than I'd ideally like, as such is there a better or faster way of doing this rather than using getAlleleIndices() to transform each Genotype into it's Indices?
-
Non-coding RNAs (ncRNAs) do not code for proteins but play important roles in numerous cellular processes including gene silencing, developmental pathways, and more. There are numerous types including microRNA (miRNA), long ncRNA (lncRNA), circular RNA (circRNA), and more. In this article, we discuss innovative ncRNA research and explore recent technological advancements that improve the study of ncRNAs.
Nobel Prize for MicroRNA Discovery
This week,...10-07-2024, 08:07 AM -
Metagenomics has improved the way researchers study microorganisms across diverse environments. Historically, studying microorganisms relied on culturing them in the lab, a method that limits the investigation of many species since most are unculturable1. Metagenomics overcomes these issues by allowing the study of microorganisms regardless of their ability to be cultured or the environments they inhabit. Over time, the field has evolved, especially with the advent...09-23-2024, 06:35 AM