Reference

Glossary

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BAM file: A binary alignment/map file which contains the positions in the reference genome where RNA-Seq reads align. This is a compressed version of the SAM file.

base pair (bp): a pair of nucleotides on opposite strands of a chromosoe at a specific genomic position. Often used in the context of genome postions e.g. “chromosome 1 at 3,000 base pairs” would indicate a position 3,000 from the start of chromosome 1.

FASTQ file: A text file containing the reads from an RNA-Seq experiment, along with base-level quality data for each read.

FastQC: (FASTQ file Quality Control) is a program which performs a variety of quality control checks on FASTQ files.

IGV: The (Integrative Genome Viewer) is a program which allows you to visualize the read alignments to the reference genome. It is used after you have aligned your reads to a reference genome and you have BAM files.

MultiQC: (MultiQC) is a program which summarizes output from multiple FastQC files to make it easier to digest the results of many samples.

read: A DNA sequence which is derived from an RNA transcript in a biological sample. These reads are often between 25 and 150 nucleotides long.

RSEM: (RNA-Seq by Expectation Maximization) is a method of quantifying gene and transcript isoform abundance which handles reads which align to multiple locations in the genome.

SAM file: A Sequence Alignment/Map file is a text file which contains the positions in the reference genome where RNA-Seq reads align. One read may align to multiple positions. It also contains the sequence of the read and its base-level quality scores.

STAR: (Spliced Transcripts Alignment to a Reference) A program which aligns RNA derived from transcripts to a reference genome in a manner which accounts for reads which cross exon splice junctions. This is referred to as a “splice-aware aligner.”