What it does

This tool converts data from GTF to a valid GFF file (scroll down for format description).

Example

• The following data in GTF:

  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";
  

• Will be converted to GFF3:

  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
  

Reference

GTF-to-GFF is part of oqtans package and cited as [1].

About formats

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:

1. seqname - The name of the sequence.
2. source - This indicating where the annotation came from.
3. feature - The name of the feature types. The following feature types are required: 'CDS', 'start_codon' and 'stop_codon'
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. end - The ending position of the feature (inclusive).
6. score - The score field indicates a degree of confidence in the feature's existence and coordinates.
7. strand - Valid entries include '+', '-', or '.'
8. 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.
9. attributes - These attributes are designed for handling multiple transcripts from the same genomic region.

GFF format General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:

1. seqid - Must be a chromosome or scaffold.
2. source - The program that generated this feature.
3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. stop - The ending position of the feature (inclusive).
6. score - A score between 0 and 1000. If there is no score value, enter ".".
7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
8. 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 '.'.
9. attributes - All lines with the same group are linked together into a single item.

Copyright

GTF-to-GFF Wrapper Version 0.6 (Apr 2015)

2009-2015 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center