## RNA-seq / Differential expression using Cufflinks

### Description

This tool will perform an analysis for differentially expressed genes using Cufflinks.

### Parameters

- Genome (Human (hg19), Mouse (mm10), Mouse (mm9), Rat (rn4)) [Human (hg19)]
- P-value cutoff (0-1) [1]
- Q-value cutoff (0-1) [1]

###
Details

This tool will perform an analysis for differentially expressed genes and isoforms using the Cufflinks algorithm. Note that only one filtering criteria should be applied for a given analysis run. When left at default settings, Cufflinks filters out unsuccessfully tested loci, as well as those with a Benjamini-Hochberg adjusted false discovery rate less than 0.05.

### Output

The analysis output consists of the following:

- de-genes-cufflinks.tsv: Table containing the results of the statistical testing for differentially expressed genes, including fold change estimates and p-values.
- de-genes-cufflinks.bed: The BED version of the results table for genes contains genomic coordinates and p-value estimates and is ideal for quick navigation in the Genome Browser.
- de-isoforms-cufflinks.tsv:Table containing the results of the statistical testing for differentially expressed isoforms, including fold change estimates and p-values.
- de-isoform-cufflinks.bed: The BED version of the results table for isoforms contains genomic coordinates and p-value estimates and is ideal for quick navigation in the Genome Browser.
- cufflinks.log: Contains useful information of the analysis run.

###
References

This tool uses the Cufflinks package for statistical analysis. Please read the following article for more detailed information:

Trapnell C, Williams BA, Pertea G, Mortazavi A, Kwan G, van Baren MJ, Salzberg SL, Wold BJ, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010 May;28(5):511-5.