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    GFF/GTF File Format - Definition and supported options

    The GFF (General Feature Format) format consists of one line per feature, each containing 9 columns of data, plus optional track definition lines. The following documentation is based on the Version 2 specifications.

    The GTF (General Transfer Format) is identical to GFF version 2.

    Fields

    Fields must be tab-separated. Also, all but the final field in each feature line must contain a value; "empty" columns should be denoted with a '.'

    1. seqname - name of the chromosome or scaffold; chromosome names can be given with or without the 'chr' prefix. Important note: the seqname must be one used within WormBase ParaSite, i.e. a standard chromosome name or a WormBase ParaSite identifier such as a scaffold ID, without any additional content such as species or assembly. See the example GFF output below.
    2. source - name of the program that generated this feature, or the data source (database or project name)
    3. feature - feature type name, e.g. Gene, Variation, Similarity
    4. start - Start position of the feature, with sequence numbering starting at 1.
    5. end - End position of the feature, with sequence numbering starting at 1.
    6. score - A floating point value.
    7. strand - defined as + (forward) or - (reverse).
    8. frame - One of '0', '1' or '2'. '0' indicates that the first base of the feature is the first base of a codon, '1' that the second base is the first base of a codon, and so on..
    9. attribute - A semicolon-separated list of tag-value pairs, providing additional information about each feature.

    Sample GTF output from WormBase ParaSite data dump:

    1 transcribed_unprocessed_pseudogene  gene        11869 14409 . + . gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; 
1 processed_transcript                transcript  11869 14409 . + . gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_sourc e "havana"; gene_biotype "transcribed_unprocessed_pseudogene"; transcript_name "DDX11L1-002"; transcript_source "havana";

    Sample GFF output from WormBase ParaSite export:

    X	Ensembl	Repeat	2419108	2419128	42	.	.	hid=trf; hstart=1; hend=21
X	Ensembl	Repeat	2419108	2419410	2502	-	.	hid=AluSx; hstart=1; hend=303
X	Ensembl	Repeat	2419108	2419128	0	.	.	hid=dust; hstart=2419108; hend=2419128
X	Ensembl	Pred.trans.	2416676	2418760	450.19	-	2	genscan=GENSCAN00000019335
X	Ensembl	Variation	2413425	2413425	.	+	.	
X	Ensembl	Variation	2413805	2413805	.	+	.

    Track lines

    Although not part of the formal GFF specification, the WormBase ParaSite browser will use track lines to further configure sets of features. Track lines should be placed at the beginning of the list of features they are to affect.

    The track line consists of the word 'track' followed by space-separated key=value pairs - see the example below. Valid parameters used by the WormBase ParaSite browser are:

    • name - unique name to identify this track when parsing the file
    • description - Label to be displayed under the track in Region in Detail
    • priority - integer defining the order in which to display tracks, if multiple tracks are defined.

    More information

    For more information about this file format, see the documentation on the Sequence Ontology website.