## RNA-seq / Compare assembled transcripts to reference annotation using Cuffcompare

### Description

Each sample is matched against the reference, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. You can supply your own GTF or use one of the provided ones.

### Parameters

- Chromosome names in my GTF files look like (chr1, 1) [1]
- Annotation GTF" TYPE (Human (hg19), Mouse (mm9), Mouse (mm10), Rat (rn4)) [Human (hg19)]
- Ignore non-overlapping reference transcripts (yes, no) [no]

### Details

Cufflinks includes a program that you can use to help analyze the transfrags you assemble. The program cuffcompare helps you:

- Compare your assembled transcripts to a reference annotation
- Track Cufflinks transcripts across multiple experiments (e.g. across a time course)

### Output

The analysis output consists of the following:

- cuffcmp.refmap.tsv
- cuffcmp.tmap.tsv
- cuffcmp.combined.gtf
- cuffcmp.loci.tsv
- cuffcmp.stats.txt
- cuffcmp.tracking.tsv

Please see Cufflinks documentation for details of output files.

### 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.