Reference: RNA-seq analysis terms & methods

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

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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
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Introduction to RNA-seq

RNA sequencing (RNA-seq) is a popular method for measuring gene expression
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What QC information does Pluto provide for RNA-seq analysis?

Uploading FASTQs will output a detailed MultiQC report
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What is Glimma?

Interactive graphics from limma
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Where does variance come from in RNA-seq data?

Differences in measurements between samples in an experiment
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What is a reference genome?

A digital nucleic acid database representing a gene set for an idealized organism.
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What is EdgeR?

Empirical analysis of differential gene expression (DGE) in R
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What is the read-count?

Total amount of reads in a sample
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What is RPKM?

Reads per kilobase of transcript per million reads
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What is TPM?

Transcripts per million fragments sequenced
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What is depth of sequencing?

Total number of reads in a sample.
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What is paired-end sequencing?

Technique used to increase the sequence coverage by sequencing a fragment from both ends.
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What is multiplexing?

Combining multiple samples into one sequencing experiment
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What are adapters?

Specific sequences that are added to the cDNA fragments during RNAseq library preparation
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What is voom?

Mean-variance modeling at the observational level
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What is DESeq2?

Differential expression analysis package
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What is SortMeRNA?

Ribosomal RNA removal tool.
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What is FPKM?

Fragments per kilobase of transcript per million reads.
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What is RSeQC?

Quality control of RNA-seq data.
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What is SAMtools?

A package of utilities to manipulate large RNA-sequencing files in SAM format.
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What is RSEM?

Transcript abundance quantification tool
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What is Kallisto?

Fast and reliable pseudo-alignment platform
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What is STAR?

Spliced Transcripts Alignment to a Reference
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What is Trim Galore?

Adapter and quality trimming.
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What is a FASTQ file?

A text file that contain the sequence information and quality scores per read
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What is FASTQC?

Checks the quality of the raw reads.
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