Reference: Analysis terms & methods

Statistical tests for comparing groups of samples

Commonly used tests include the t-test, ANOVA, and Kruskal Wallace

Written by Rani Powers, PhD
Updated over a week ago

SD versus SEM

Choosing the appropriate statistical analysis for your data.

Written by MacKenzie Demmel
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What is fold change?

Ratio that describes a change in a measured value (e.g. gene expression)

Written by Rani Powers, PhD
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Introduction to RNA-seq

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

Written by Rani Powers, PhD
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What QC information does Pluto provide for RNA-seq analysis?

Uploading FASTQs will output a detailed MultiQC report

Written by Rani Powers, PhD
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What is Glimma?

Interactive graphics from limma

Written by MacKenzie Demmel
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Where does variance come from in RNA-seq data?

Differences in measurements between samples in an experiment

Written by Andrew Goodspeed
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What is a reference genome?

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

Written by Rani Powers, PhD
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What is EdgeR?

Empirical analysis of differential gene expression (DGE) in R

Written by MacKenzie Demmel
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What is the read-count?

Total amount of reads in a sample

Written by Rani Powers, PhD
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What is RPKM?

Reads per kilobase of transcript per million reads

Written by Rani Powers, PhD
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What is TPM?

Transcripts per million fragments sequenced

Written by Rani Powers, PhD
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What is depth of sequencing?

Total number of reads in a sample.

Written by Rani Powers, PhD
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What is paired-end sequencing?

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

Written by Rani Powers, PhD
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What is multiplexing?

Combining multiple samples into one sequencing experiment

Written by Rani Powers, PhD
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What are adapters?

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

Written by Rani Powers, PhD
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What is voom?

Mean-variance modeling at the observational level

Written by Rani Powers, PhD
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What is DESeq2?

Differential expression analysis package

Written by Rani Powers, PhD
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What is SortMeRNA?

Ribosomal RNA removal tool.

Written by Rani Powers, PhD
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What is FPKM?

Fragments per kilobase of transcript per million reads.

Written by Rani Powers, PhD
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What is RSeQC?

Quality control of RNA-seq data.

Written by Rani Powers, PhD
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What is SAMtools?

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

Written by Rani Powers, PhD
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What is RSEM?

Transcript abundance quantification tool

Written by Rani Powers, PhD
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What is Kallisto?

Fast and reliable pseudo-alignment platform

Written by Rani Powers, PhD
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What is STAR?

Spliced Transcripts Alignment to a Reference

Written by Rani Powers, PhD
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What is Trim Galore?

Adapter and quality trimming.

Written by Rani Powers, PhD
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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