RNA-seq / Differential expression using Cufflinks

Description

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

Parameters


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:


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.