Salīdzināt metodes

	Variantu identificēšana	RNA-seq diferenciālās ekspresijas
Nozare	Bioinformātika	Bioinformātika
Saime	Process / pipeline	Process / pipeline
Izcelsmes gads	2009–2010 (modern high-throughput era)	2008–2010 (RNA-seq DE methodology established)
Autors	Li et al. (SAMtools/bcftools, 2009); McKenna et al. (GATK, 2010)	Multiple groups; foundational methods from Anders & Huber (DESeq, 2010), Robinson, McCarthy & Smyth (edgeR, 2010)
Tips	Computational genomics pipeline	Quantitative genomics pipeline
Pirmavots	McKenna, A., Hanna, M., Banks, E., Sivachenko, A., Cibulskis, K., Kernytsky, A., ... & DePristo, M. A. (2010). The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data. Genome Research, 20(9), 1297–1303.	Love, M. I., Huber, W., & Anders, S. (2014). Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2. Genome Biology, 15(12), 550.
Citi nosaukumi	SNP calling, genotyping from sequencing, mutation detection, variant detection	RNA-seq DE analysis, transcriptomic differential expression, bulk RNA-seq DE, DEA
Saistītās	6	6
Kopsavilkums	Variant calling is the computational process of identifying positions in a sequenced genome that differ from a reference sequence — including single nucleotide polymorphisms (SNPs), small insertions and deletions (indels), and structural variants. It transforms aligned sequencing reads into an interpretable catalogue of genetic differences, forming the foundation for population genetics, disease-gene discovery, and clinical genomics applications.	RNA-seq differential expression (DE) analysis identifies genes whose transcript abundance differs significantly between two or more biological conditions — for example, treated versus control, or diseased versus healthy tissue. Starting from raw sequencing reads, the pipeline moves through alignment, count-based normalization, statistical modeling of count dispersion, hypothesis testing, and multiple-testing correction to produce a ranked list of differentially expressed genes accompanied by fold-change estimates and adjusted p-values.