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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)

Cuffcompare takes Cufflinks' GTF output as input, and optionally can take a "reference" annotation (such as from Ensembl)

Version 1.0
Bundle sequencing
Specialties generic
Authors Alejandra Cervera (alejandra.cerverataboada@helsinki.fi)
Issue tracker View/Report issues
Requires Cufflinks ; installer (bash)
Source files component.xml Cuffcompare.java
Usage Example with default values

This component is not being used anymore, last update to the software was 4 years ago.

Type parameters (generics)


Name Type Mandatory Description
arrayIn Array<T1> (generic) Mandatory An array with the transcripts to be compared.
reference_annotation GTF Optional An optional "reference" annotation GFF file. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. See the refmap and tmap output file descriptions below.
seq_dir BinaryFolder Optional Causes cuffcompare to look into for fasta files with the underlying genomic sequences (one file per contig) against which your reads were aligned for some optional classification functions. For example, Cufflinks transcripts consisting mostly of lower-case bases are classified as repeats. Note that seq_dir must contain one fasta file per reference chromosome, and each file must be named after the chromosome, and have a .fa or .fasta extension.


Name Type Description
arrayOut Array<T1> (generic) An array with all output files from cuffcompare. Check cuffcompare documentation for details.


Name Type Default Description
R boolean false If -r was specified, this option causes cuffcompare to ignore reference transcripts that are not overlapped by any transcript in one of cuff1.gtf,...,cuffN.gtf. Useful for ignoring annotated transcripts that are not present in your RNA-Seq samples and thus adjusting the "sensitivity" calculation in the accuracy report written in the outprefix file
contained boolean false Enables the "contained" transcripts to be also written in the outprefix.combined.gtffile, with the attribute "contained_in" showing the first container transfrag found. By default, without this option, cuffcompare does not write in that file isoforms that were found to be fully contained/covered (with the same compatible intron structure) by other transfrags in the same locus.
help boolean false Prints the help message and exits.
outprefix string "" All output files created by Cuffcompare will have this prefix (e.g. outprefix.loci, outprefix.tracking, etc.). If this option is not provided the default output prefix being used is: "cuffcmp"
verbose boolean false Print lots of status updates and other diagnostic information.

Test cases

Test case Parameters IN
case1 properties arrayIn reference_annotation seq_dir (missing)

# Testing cufflinks component

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