GTF_update.rst

Preparing the GTF format file

The current RiboCode version supports the standard GTF format, and it also requires the GTF file to be satisfied with three-level hierarchy annotations (genes contain transcripts that contain exons and optionally, a CDS). This type of file can be obtained from ENSEMBL/GENCODE database. Those from other source or the custom GTF file may lack the gene and transcript annotation information. RiboCode provide a command "GTFupdate" which can add these two information for GTF file:

GTFupdate original.gtf > updated.gtf

Example:

original GTF:

1 unknown exon 11874 12227 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018.2";

1 unknown exon 12613 12721 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018.2";

1 unknown exon 13221 14409 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018.2";

after updating:

1 unknown gene 11874 14409 . + . gene_id "DDX11L1"; gene_name "DDX11L1";

1 unknown transcript 11874 14409 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018.2";

1 unknown exon 11874 12227 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018.2";

1 unknown exon 12613 12721 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018.2";

1 unknown exon 13221 14409 . + . gene_id "DDX11L1"; gene_name "DDX11L1"; transcript_id "NR_046018.2";

the standard GTF format

see detail in this website: https://en.wikipedia.org/wiki/GENCODE

column-number +	content
1 +	chromosome
2 +	source (not used)
3 +	feature type
4 +	genomic start location
5 +	genomic end location
6 +	score(not used)
7 +	genomic strand
8 +	genomic phase(not used)
9 +	attributes (see below)

Description of attributes in 9th column of the GTF file

• gene_id
• transcript_id
• gene_type (optional)
• gene_name (optional)
• transcript_id (optional)
• transcript_type (optional)
• level (optional)
• cdds (optional)