## RNA-seq / Merge transcript assemblies with Cuffmerge

### Description

This tool merges transcript assemblies with Cuffmerge.

### Parameters

Exclude transcripts with duplicate ids (yes, no) [no]

### 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.

Cufflinks produces sometimes GTF files which contain duplicate transcript identifiers. In this case Cuffmerge will terminate and produce a log file reporting the problem. You can exclude duplicate identifiers by turning the parameter on. This way Cuffmerge will produce a merged GTF file and report in the log file how many transcripts were removed from each input file.

### Output

The analysis output consists of the following:

- merged.gtf: A GTF file that contains an assembly that merges together the input assemblies.
- cuffmerge.log: A log file containing possible error messages or the number of excluded transcripts.

### 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.