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model-format.md

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Transcript model format

GTF format

Genome transcript annotation submissions are in GTF format (see GTF2.2 and Ensembl GFF/GTF File Format).

Only exon features are used, and exons of a given transcript are linked together by the transcript_id attribute. Gaps of at least XX bases between exons are assumed to be introns. Smaller gaps are closed, combining the exon features. The evaluation ignores other features that are provided, however, they will still be validated for syntax and consistency.

The standard GTF fields have the following restrictions:

  • seqname - Must be one of the sequence identifiers in the LRGAPS reference genomes.
  • source - Ignored.
  • feature - Only exon is used. Other types of records are ignored.
  • start - Standard, one-based start position.
  • end - Standard, one-based end position.
  • score - Ignored.
  • strand - Must be specified as +, - or . on exon features, other features types may be validated.
  • frame - Should be . on exon features, but not valid. Others features types may be validated.
  • attributes:
    • transcript_id - Required for all exon features and assigned by the submitter.
    • gene_id - Required for all exon features. While not evaluated by LRGASP, it is unclear if this is require by GTF. Some tools, such as the UCSC Genome Browse and command-line tools, will fail without gene_id. The assigned gene_id doesn't have to represent an actual gene. However, it must not reflect impossible genes, such as those on different chromosomes. If gene assignment are not supported, it suggest that each transcript is assigned it own gene_id, which maybe the same as the transcript_id.
    • reference_transcript_id - Optional, used to indicate the transcript is a reference call for the specified reference transcript.
    • reference_gene_id - Optional, used to indicate the gene is a reference call for the specified reference gene. This maybe specified without a reference_transcript_id attribute if the models is not as assigned to a specific transcript within the gene.
    • Other attributes are ignored

All of the attributes specified above must be repeated on all exons of a transcript with the same value. An example models submission GTF file is at models.gtf.

File naming

Files must be named xxx.gtf (FIXME defend better) and maybe compressed with gzip and then have a name in the form xxx.gtf.gz.

Validation

A validation program is provide dfor the annotation GTFs, and the submitter must run this before submitting the file.