GFF AND GTF

panhoy 2014-06-11

展开全文

GFF (General Feature Format) lines are based on the Sanger GFF2 specification. GFF lines have nine required fields that must be tab-separated. If the fields are separated by spaces instead of tabs, the track will not display correctly. For more information on GFF format, refer to Sanger's GFF page.

Note that there is also a GFF3 specification that is not currently supported by the Browser. All GFF tracks must be formatted according to Sanger's GFF2 specification.

If you would like to obtain browser data in GFF (GTF) format, please refer to Genes in gtf or gff format on the Wiki.

Here is a brief description of the GFF fields:

seqname - The name of the sequence. Must be a chromosome or scaffold.
source - The program that generated this feature.
feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
start - The starting position of the feature in the sequence. The first base is numbered 1.
end - The ending position of the feature (inclusive).
score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). If there is no score value, enter ".".
strand - Valid entries include '+', '-', or '.' (for don't know/don't care).
frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
group - All lines with the same group are linked together into a single item

GFF (General Feature Format) lines are based on the Sanger GFF2 specification. GFF lines have nine required fields that must be tab-separated. If the fields are separated by spaces instead of tabs, the track will not display correctly. For more information on GFF format, refer to Sanger's GFF page.

Note that there is also a GFF3 specification that is not currently supported by the Browser. All GFF tracks must be formatted according to Sanger's GFF2 specification.

If you would like to obtain browser data in GFF (GTF) format, please refer to Genes in gtf or gff format on the Wiki.

Here is a brief description of the GFF fields:
seqname - The name of the sequence. Must be a chromosome or scaffold.
source - The program that generated this feature.
feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
start - The starting position of the feature in the sequence. The first base is numbered 1.
end - The ending position of the feature (inclusive).
score - A score between 0 and 1000. If the track line useScore attribute is set to 1 for this annotation data set, the score value will determine the level of gray in which this feature is displayed (higher numbers = darker gray). If there is no score value, enter ".".
strand - Valid entries include '+', '-', or '.' (for don't know/don't care).
frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
group - All lines with the same group are linked together into a single item.

Example:

browser position chr22:10000000-10025000 browser hide all track name=regulatory description="TeleGene(tm) Regulatory Regions" visibility=2 chr22 TeleGene enhancer 10000000 10001000 500 + . touch1 chr22 TeleGene promoter 10010000 1001010

GTF format

GTF (Gene Transfer Format) is a refinement to GFF that tightens the specification. The first eight GTF fields are the same as GFF. The group field has been expanded into a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space.

The attribute list must begin with the two mandatory attributes:

gene_id value - A globally unique identifier for the genomic source of the sequence.
transcript_id value - A globally unique identifier for the predicted transcript.

Example:
Here is an example of the ninth field in a GTF data line:

gene_id "Em:U62317.C22.6.mRNA"; transcript_id "Em:U62317.C22.6.mRNA"; exon_number 1

The Genome Browser groups together GTF lines that have the same transcript_id value. It only looks at features of type exon and CDS.

For more information on this format, see http://mblab./GTF2.html.

If you would like to obtain browser data in GTF format, please refer to Genes in gtf or gff format on the Wiki.