Reference: RNA-seq analysis terms & methods

Details and useful links to tools that Pluto uses in its RNA-seq analysis pipeline

26 articles in this collection
Written by Rani Powers, PhD, MacKenzie Demmel, and Andrew Goodspeed

Standard RNA-seq parameters in Pluto

Methods for the out-of-the-box RNA-seq pipeline using STAR & RSEM

Written by Andrew Goodspeed
Updated over a week ago

Introduction to RNA-seq

RNA sequencing (RNA-seq) is a popular method for measuring gene expression

Written by Rani Powers, PhD
Updated over a week ago

What QC information does Pluto provide for RNA-seq analysis?

Uploading FASTQs will output a detailed MultiQC report

Written by Rani Powers, PhD
Updated over a week ago

What is Glimma?

Interactive graphics from limma

Written by MacKenzie Demmel
Updated over a week ago

Where does variance come from in RNA-seq data?

Differences in measurements between samples in an experiment

Written by Andrew Goodspeed
Updated over a week ago

What is a reference genome?

A digital nucleic acid database representing a gene set for an idealized organism.

Written by Rani Powers, PhD
Updated over a week ago

What is EdgeR?

Empirical analysis of differential gene expression (DGE) in R

Written by MacKenzie Demmel
Updated over a week ago

What is the read-count?

Total amount of reads in a sample

Written by Rani Powers, PhD
Updated over a week ago

What is RPKM?

Reads per kilobase of transcript per million reads

Written by Rani Powers, PhD
Updated over a week ago

What is TPM?

Transcripts per million fragments sequenced

Written by Rani Powers, PhD
Updated over a week ago

What is depth of sequencing?

Total number of reads in a sample.

Written by Rani Powers, PhD
Updated over a week ago

What is paired-end sequencing?

Technique used to increase the sequence coverage by sequencing a fragment from both ends.

Written by Rani Powers, PhD
Updated over a week ago

What is multiplexing?

Combining multiple samples into one sequencing experiment

Written by Rani Powers, PhD
Updated over a week ago

What are adapters?

Specific sequences that are added to the cDNA fragments during RNAseq library preparation

Written by Rani Powers, PhD
Updated over a week ago

What is voom?

Mean-variance modeling at the observational level

Written by Rani Powers, PhD
Updated over a week ago

What is DESeq2?

Differential expression analysis package

Written by Rani Powers, PhD
Updated over a week ago

What is SortMeRNA?

Ribosomal RNA removal tool.

Written by Rani Powers, PhD
Updated over a week ago

What is FPKM?

Fragments per kilobase of transcript per million reads.

Written by Rani Powers, PhD
Updated over a week ago

What is RSeQC?

Quality control of RNA-seq data.

Written by Rani Powers, PhD
Updated over a week ago

What is SAMtools?

A package of utilities to manipulate large RNA-sequencing files in SAM format.

Written by Rani Powers, PhD
Updated over a week ago

What is RSEM?

Transcript abundance quantification tool

Written by Rani Powers, PhD
Updated over a week ago

What is Kallisto?

Fast and reliable pseudo-alignment platform

Written by Rani Powers, PhD
Updated over a week ago

What is STAR?

Spliced Transcripts Alignment to a Reference

Written by Rani Powers, PhD
Updated over a week ago

What is Trim Galore?

Adapter and quality trimming.

Written by Rani Powers, PhD
Updated over a week ago

What is a FASTQ file?

A text file that contain the sequence information and quality scores per read

Written by Rani Powers, PhD
Updated over a week ago

What is FASTQC?

Checks the quality of the raw reads.

Written by Rani Powers, PhD
Updated over a week ago