Our GFF reader will ignore redundant features like start_codon, stop_codon when whole CDS features were provided, or *UTR features when whole exon features were also given. TopHat and Cufflinks generally expect exon features to define a transcript structure, with optional CDS features to specify the coding segments.
Ensembl) place a “human readable” gene name/symbol in the gene_name attribute, like a HUGO symbol (while gene_id might be just an automatically generated numeric identifier for the gene). An optional gene_name attribute, if found, will be taken and shown as a symbolic gene name or short-form abbreviation (e.g. GTF2Īs seen in the GTF2 specification, the transcript_id attribute is also required by our GFF parser, and a gene_id attribute, though not strictly required in our programs, is very useful for grouping alternative transcripts under a gene/locus identifier. Here are a few notes about the way these formats are interpreted by the Cufflinks programs. GFF has many versions, but the two most popular that are supported by Cufflinks (and other programs in the Tuxedo suite, like Tophat) are GTF2 (Gene Transfer Format, described here) and GFF3 (defined here). Some of the Cufflinks modules take as input a file (or more) containing known gene annotations or other transcript data in GFF format (General Feature Format). Output formats used in the Cufflinks suite.
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