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GTF

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

A globally unique identifier for the genomic source of the sequence.

 
 transcript_id

A globally unique identifier for the predicted transcript.

Check the nineth GTF field of the sample annotation of the workshop:

cut -f9 ~ngs00/refs/mm65.long.ok.gtf | head -1
gene_id "ENSMUSG00000076490"; transcript_id "ENSMUST00000103291"; exon_number "1"; gene_name "Trbc1"; gene_type "IG_C_gene"; transcript_name "Trbc1-201"; protein_id "ENSMUSP00000100099"; transcript_type "IG_C_gene";

Look at the first line:

head -1 ~ngs00/refs/mm65.long.ok.gtf | tr '\t' '\n'
chr6 (1)
ENSEMBL (2)
CDS (3)
41488217 (4)
41488591 (5)
. (6)
+ (7)
2 (8)
gene_id "ENSMUSG00000076490"; transcript_id "ENSMUST00000103291"; exon_number "1"; gene_name "Trbc1"; gene_type "IG_C_gene"; transcript_name "Trbc1-201"; protein_id "ENSMUSP00000100099"; transcript_type "IG_C_gene"; (9)

  1. seqname - The name of the sequence. Must be a chromosome or scaffold.

  2. source - The program that generated this feature.

  3. feature - The name of this type of feature. Some examples of standard feature types are CDS, start_codon, stop_codon, and exon.

  4. start - The starting position of the feature in the sequence (1-based).

  5. end - The ending position of the feature (inclusive).

  6. score - A score between 0 and 1000.

  7. strand - Valid entries include +, -, or . (for don’t know/don’t care).

  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. If the feature is not a coding exon, the value should be ..

  9. group - All lines with the same group are linked together into a single item. Note the gene_id and transcript_id mandatory attributes.

Feature types

The third field in the GFF specification represents feature type for the line. In addition to the standard features mentioned above there can be intron, gene and transcript.

Look for the first of each feature in the sample annotation of the workshop:

awk '$3=="intron"' ~ngs00/refs/mm65.long.ok.gtf | head -1
chr17	ENSEMBL	#intron#	46893352	46893968	.	-	.	gene_id "ENSMUSG00000036858"; transcript_id "ENSMUST00000041012"; exon_number "3"; gene_name "Ptcra"; gene_type "IG_C_gene"; transcript_name "Ptcra-201"; transcript_type "IG_C_gene";
awk '$3=="gene"' ~ngs00/refs/mm65.long.ok.gtf | head -1
chr4	ENSEMBL	#gene#	116791824	116798271	.	-	.	gene_id "ENSMUSG00000073771"; transcript_id "ENSMUSG00000073771"; gene_type "protein_coding"; gene_status "NULL"; gene_name "Btbd19"; transcript_type "protein_coding"; transcript_status "NULL"; transcript_name "Btbd19";
awk '$3=="transcript"' ~ngs00/refs/mm65.long.ok.gtf | head -1
chr13	ENSEMBL	transcript	19305972	19308487	.	+	.	gene_id "ENSMUSG00000076749"; transcript_id "ENSMUST00000103558"; exon_number "1"; gene_name "Gm17004"; gene_type "IG_C_gene"; transcript_name "Gm17004-201"; transcript_type "IG_C_gene";