Analyzes the transcribed fragments in an assembly
Author: Cole Trapnell et al, University of Maryland Center for Bioinformatics and Computational Biology
Algorithm Version: Cufflinks 2.0.2
Cufflinks.cuffcompare helps analyze the transcribed fragments (transfrags) in an assembly by:
Cufflinks was created at the University of Maryland Center for Bioinformatics and Computational Biology. This document is adapted from the Cufflinks documentation for release 2.0.2. For more information about Cufflinks.cuffcompare, see the Cufflinks documentation.
Cufflinks.cuffcompare requires at least one Cufflinks' GTF output file as input, and optionally can also take a "reference" annotation GTF/GFF file such as from Ensembl. For more information on the GTF/GFF format, see the specification.
The Cuffcompare tool provides a number of additonal options and switches that are not directly available through this module's paramters. The additional.cuffcompare.options parameter is provided to pass these through if you feel that you need them. To use it, simply specify the extra option(s) along with any arguments in the input text field separated by spaces. At this time, this parameter unfortunately does not easily support options which require a file argument. Check the Cufflinks manual for more details of the available options. Also note that there may be additional undocumented options; manually running the cufflinks executable at the command line with no arguments may show even more options. If you feel that a particular missing option would be of broad general interest, please contact the GenePattern team and we will look into adding it. Use of this parameter is recommended for expert use only; use it at your own discretion. The GenePattern team does not explicitly test all of the possible options that may be passed through using this parameter and can only provide limited support.
Trapnell C, Hendrickson D,Sauvageau S, Goff L, Rinn JL, Pachter L. Differential analysis of gene regulation at transcript resolution with RNA-seq. Nature Biotechnology. 2013;31:46-53.
Trapnell C, Roberts A, Goff L, Pertea G, Kim D, Kelley DR, Pimentel H, Salzberg SL, Rinn JL, Pachter L. Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks. Nature Protocols 2012;7;562–578.
Roberts A, Pimentel H, Trapnell C, Pachter L. Identification of novel transcripts in annotated genomes using RNA-Seq. Bioinformatics. 2011 Sep 1;27(17):2325-9.
Trapnell C, Williams BA, Pertea G, Mortazavi AM, Kwan G, van Baren MJ, Salzberg SL, Wold B, Pachter L. Transcript assembly and quantification by RNA-Seq reveals unannotated transcripts and isoform switching during cell differentiation. Nat Biotechnol. 2010;28:511-515.
Trapnell C, Pachter L, Salzberg SL. TopHat: discovering splice junctions with RNA-Seq. Bioinformatics. 2009;25:1105-1111.
Langmead B, Trapnell C, Pop M, Salzberg SL. Ultrafast and memory-efficient alignment of short DNA sequences to the human genome. Genome Biol. 2009;10:R25.
|input file *||One or more GTF file output(s) from Cufflinks|
|output prefix||A prefix for the module output|
|reference GTF||A reference annotation GTF|
|exclude transcripts||Whether to ignore reference transcripts that are not overlapped by any transcript in the input files. This takes effect only if a reference GTF is provided.|
|reference genome file||Fasta file or zip of fasta files against which your reads were aligned|
|additional cuffcompare options||Additional options to be passed along to the Cuffcompare program at the command line. This parameter gives you a means to specify otherwise unavailable Cuffcompare options and switches not supported by the module; check the Cufflinks manual for details. Note that the information at this link may refer to a subsequent version of Cufflinks. Recommended for experts only; use this at your own discretion.|
* - required
The following may be useful for advanced users who wish to use the additional.cuffcompare.options parameter. This is the 'usage' output from running cuffcompare at the command-line, which gives a list of all of the available options and switches. Note that this was generated by Cuffcompare v2.0.2 and that the options here may differ from the documentation provided online at the Cufflinks website due to subsequent version updates.
cuffcompare v2.0.2 (3524M)
A reference annotation file in GTF format. Each sample is matched against this file, and sample isoforms are tagged as overlapping, matching, or novel where appropriate. These reference annotation files can be downloaded for many genomes from sites like UCSC Genome Browser. The GenePattern FTP site hosts a number of reference annotation GTFs, available in a dropdown selection (requires GenePattern 3.7.0+).
For more information on the GTF format, see the specification.
Fasta file or zip of fasta files against which your reads were aligned. If supplied, cuffcompare will use this for some optional classification functions. If a multifasta file, all contigs should be present. If a zip, this must contain one fasta file per reference chromosome, and each file must be named after the chromosome and have a .fa or .fasta extension. For more information on the FASTA format, see this description.
The GenePattern FTP site hosts a number of reference genomes, available in a dropdown selection (requires GenePattern 3.7.0+).
For more information about Cufflinks.cuffcompare output files, see the Cufflinks documentation
|7||2014-02-14||Added a parameter to allow the user to pass through extra Cuffcompare options|
|6||2013-09-25||Added dynamic GTF and genome file selectors and HTML-based documentation|
|5||2013-07-22||Updated to Cufflinks.cuffcompare version 2.0.2|
|4||2012-07-06||Fixed syntax error.|
|2||2012-01-13||Updated to Cufflinks.cuffcompare version 1.3.0|