RNA-seq / Merge transcript assemblies with Cuffmerge

Description

This tool merges transcript assemblies with Cuffmerge.

Parameters

None.

Details

Given several transcript GTF files obtained by Cufflinks, Cuffmerge merges them into one. The merged GTF file can be used in differential expression analysis with Cuffdiff.

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.