What it does
This tool converts data from GFF3 format to GTF format.
Example
The following data in GFF3 format:
17 protein_coding gene 7255208 7258258 . + . ID=ENSG00000213859;Name=KCTD11 17 protein_coding mRNA 7255208 7258258 . + . ID=ENST00000333751;Name=KCTD11-001;Parent=ENSG00000213859 17 protein_coding protein 7256262 7256960 . + . ID=ENSP00000328352;Name=KCTD11-001;Parent=ENST00000333751 17 protein_coding five_prime_UTR 7255208 7256261 . + . Parent=ENST00000333751 17 protein_coding CDS 7256262 7256960 . + 0 Name=CDS:KCTD11;Parent=ENST00000333751,ENSP00000328352 17 protein_coding three_prime_UTR 7256961 7258258 . + . Parent=ENST00000333751 17 protein_coding exon 7255208 7258258 . + . Parent=ENST00000333751
Will be converted to GTF format:
17 protein_coding exon 7255208 7258258 . + . gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; 17 protein_coding CDS 7256262 7256957 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; protein_id "ENSP00000328352"; 17 protein_coding start_codon 7256262 7256264 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001"; 17 protein_coding stop_codon 7256958 7256960 . + 0 gene_id "ENSG00000213859"; transcript_id "ENST00000333751"; exon_number "1"; gene_name "KCTD11"; transcript_name "KCTD11-001";
About formats
GFF3 format General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF3 lines have nine tab-separated fields:
- seqid - Must be a chromosome or scaffold.
- source - The program that generated this feature.
- type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
- start - The starting position of the feature in the sequence. The first base is numbered 1.
- stop - The ending position of the feature (inclusive).
- score - A score between 0 and 1000. If there is no score value, enter ".".
- strand - Valid entries include '+', '-', or '.' (for don't know/care).
- phase - 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 '.'.
- attributes - All lines with the same group are linked together into a single item.
GTF format Gene Transfer Format, it borrows from GFF, but has additional structure that warrants a separate definition and format name. GTF lines have nine tab-seaparated fields:
- seqname - The name of the sequence.
- source - This indicating where the annotation came from.
- feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
- 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 - The score field indicates a degree of confidence in the feature's existence and coordinates.
- strand - Valid entries include '+', '-', or '.'
- 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.
- attributes - These attributes are designed for handling multiple transcripts from the same genomic region.
This tool is a part of the MLB Group at Friedrich Miescher Laboratory of the Max Planck Society. Copyright (C) 2010 Vipin T. Sreedharan (vipin.ts@tuebingen.mpg.de)