# 10_DE_analysis

By Yan Li

PhD in Bioinformatics, University of Liverpool

## RNA-seq

## Popular software

- Mapping:
`Tophat2`

,`HISAT2`

- Reads counting:
`HTSeq-counts`

,`Cufflink`

- Defferential Expressing analysis:
`EdgeR`

,`DEseq2`

,`limma`

- GO enrichment:
`DAVID`

,`g.profiler`

## Terminology

- RPKM: Reads Per Kilobase per Million mapped read.
- RPKM = 10^9 * N / L * 1 / C
- N: the total number of reads mapped to a transcript
- C: the number of reads mapped to a gene
- L: the length of the gene

- GO: Gene ontology

## Basic Statistics

- P-value and False discovery rate (FDR) adjusted p values
- a p-value of 0.05 implies that 5% of all tests will result in false positives.
- An FDR adjusted p-value (or q-value) will result in fewer false positives.

- Fold Change
- Fold change is a measure describing how much a quantity changes going from an initial to a final value.