## 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:

- merged.gtf: A GTF file that contains an assembly that merges together the input assemblies.

### 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.