Building a TxDb object

Here is an example of how to build resources from Gene transfer format (GTF) files.

Structure is as GFF, so the fields are: <seqname> <source> <feature> <start> <end> <score> <strand> <frame> [attributes] [comments]

We can view the information in the GTF file we downloaded here.

/home/USER/db/refanno/gencode.v33.annotation.gtf
##description: evidence-based annotation of the human genome (GRCh38), version 33 (Ensembl 99)
##provider: GENCODE
##contact: gencode-help@ebi.ac.uk
##format: gtf
##date: 2019-12-13
chr1	HAVANA	gene	11869	14409	.	+	.	gene_id "ENSG00000223972.5"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; level 2; hgnc_id "HGNC:37102"; havana_gene "OTTHUMG00000000961.2";
chr1	HAVANA	transcript	11869	14409	.	+	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1	HAVANA	exon	11869	12227	.	+	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 1; exon_id "ENSE00002234944.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1	HAVANA	exon	12613	12721	.	+	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 2; exon_id "ENSE00003582793.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";
chr1	HAVANA	exon	13221	14409	.	+	.	gene_id "ENSG00000223972.5"; transcript_id "ENST00000456328.2"; gene_type "transcribed_unprocessed_pseudogene"; gene_name "DDX11L1"; transcript_type "processed_transcript"; transcript_name "DDX11L1-202"; exon_number 3; exon_id "ENSE00002312635.1"; level 2; transcript_support_level "1"; hgnc_id "HGNC:37102"; tag "basic"; havana_gene "OTTHUMG00000000961.2"; havana_transcript "OTTHUMT00000362751.1";

In /home/USER/db/refanno we execute R:

library(GenomicFeatures)

gtf <- "gencode.v33.annotation.gtf"
txdb.filename <- "gencode.v33.annotation.sqlite"

txdb <- makeTxDbFromGFF(gtf)

# We can use saveDb() to save the TxDb database (SQLite database) for later uses
saveDb(txdb, txdb.filename)

# We can use loadDb() to use the TxDb database
txdb <- loadDb(txdb.filename)
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