Genomics Glossaries

• ATAC-Seq - Assay for Transposase-Accessible Chromatin with high-throughput sequencing. The ATAC-Seq method relies on next-generation sequencing (NGS) library construction using the hyperactive transposase Tn5.  By sequencing regions of open chromatin, ATAC-Seq can help to assess genome-wide chromatin accessibility, thus uncover how chromatin packaging and other factors affect gene expression.
• aseQTLs - allele-specific expression quantitative trait loci, may result from cis-regulatory SNPs.
• ChIP-seq - ChIP-sequencing, is a method used to analyze protein interactions with DNA. The method combines chromatin immunoprecipitation (ChIP) with massively parallel DNA sequencing to identify the binding sites of DNA-associated proteins.
• CAGE - Cap analysis of gene expression, is an approach to identify and monitor the activity (transcription initiation frequency) of transcription start sites (TSSs) at single base-pair resolution across the genome.
• RAD-seq - a protocol for genotyping and discovery of single-nucleotide polymorphisms (SNPs) (Baird et al., 2008). This approach is particularly useful for genotyping when a reference genome is not available, such as in ecological studies. Restriction site associated DNA (RAD) markers are a type of genetic marker which are useful for association mapping, QTL-mapping, population genetics, ecological genetics and evolutionary genetics. The use of RAD markers for genetic mapping is often called RAD mapping. An important aspect of RAD markers and mapping is the process of isolating RAD tags, which are the DNA sequences that immediately flank each instance of a particular restriction site of a restriction enzyme throughout the genome.[1] Once RAD tags have been isolated, they can be used to identify and genotype DNA sequence polymorphisms mainly in form of single nucleotide polymorphisms (SNPs).[1] Polymorphisms that are identified and genotyped by isolating and analyzing RAD tags are referred to as RAD markers.
• eeQTL - Exon expression QTL -  study the genomic variations that are associated with splicing regulation. A stringent criterion was adopted to study gene-level eQTLs and exon-level eeQTLs for both cis- and trans- factors. (Guan et al, 2014).
• eQTL / geQTL - (gene) expression Quantitative Trait Locus, denotes the relationship between transcription and SNP. An eQTL is a locus that explains a fraction of the genetic variance of a gene expression phenotype. It essentially perform a GWAS using the expression value of the gene as a trait. It usually contains locations where there is polymorphic expression (Most people do some form of cis-eQTL analysis using only SNPs within some kMB of the TSS or TSE. Often k=0.5MB).
• mQTL / meQTL denotes the relationship between methylation and SNP.
• mQTL == Metabolomic Quantitative Trait Loci
• miRNA-seq - MicroRNA sequencing, a type of RNA-Seq, is the use of next-generation sequencing or massively parallel high-throughput DNA sequencing to sequence microRNAs, also called miRNAs. miRNA-seq differs from other forms of RNA-seq in that input material is often enriched for small RNAs. miRNA-seq allows researchers to examine tissue-specific expression patterns, disease associations, and isoforms of miRNAs, and to discover previously uncharacterized miRNAs.
• RNA-Seq (named as an abbreviation of RNA sequencing) is a sequencing technique which uses next-generation sequencing (NGS) to reveal the presence and quantity of RNA in a biological sample at a given moment, analyzing the continuously changing cellular transcriptome. Specifically, RNA-Seq facilitates the ability to look at alternative gene spliced transcripts, post-transcriptional modifications, gene fusion, mutations/SNPs and changes in gene expression over time, or differences in gene expression in different groups or treatments
• RACE - Rapid amplification of cDNA ends, is a technique used in molecular biology to obtain the full length sequence of an RNA transcript found within a cell.
• sQTL - Caused by SNPs that alter splicing or alternative splicing (AS), such as by changing the sequence-specific binding affinity of splicing factors to the pre-mRNA.
• GWAS denotes the relationship between SNP and trait.

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• RPKM - Reads Per Kilobase Million:
  • Total reads in a sample divided by 1,000,000 ➜ "per million" scaling factor (SF);
  • Divide read counts by SF(normalize for seq depth) ➜ RPM (reads per million);
  • Divide RPM by the length of the gene (kb) ➜ RPKM.
• FPKM - Fragments Per Kilobase Million):
  • Similar to RPKM but by paired-end RNA-seq fragments, where two reads can correspond to a single fragment.
• TPM - Transcripts Per Kilobase Million):
  • Divide the read counts by the length of each gene (kb) ➜ reads per kilobase (RPK)
  • Devide all RPK values in a sample by 1,000,000 ➜ "per million" scaling factor (SF);
  • Divide the RPK values by SF ➜ TPM.