Hi,

I am trying to extract the promoter regions from gencode gtf file only for "lincRNA" and "antisense" (under "gene_type" column in the gtf file downloaded from the gencode website). 

I think I need to start by using GenomicFeatures to first import the gtf file:

    library("GenomicFeatures")
    # Download the version 19 gencode gtf file from gencode website, and then load here
    txdb = makeTxDbFromGFF("file.gtf", format="gtf")

But I don't think the column in the gtf file called "gene_type" is imported. 

How can I import and select the columns "lincRNA" and "antisense" from the TxDb file?

The gtf file looks like this:

#!genome-build GRCh37.p13
#!genome-version GRCh37
#!genome-date 2009-02
#!genome-build-accession NCBI:GCA_000001405.14
#!genebuild-last-updated 2013-09

chr16    HAVANA    gene    53069602    53086785    .    -    .    gene_id "ENSG00000261550.1"; transcript_id "ENSG00000261550.1"; gene_type "antisense"; gene_status "NOVEL"; gene_name "RP11-467J12.4"; transcript_type "antisense"; transcript_status "NOVEL"; transcript_name "RP11-467J12.4"; level 2; havana_gene "OTTHUMG00000173186.1";

chr5    HAVANA    transcript    10493639    10502840    .    -    .    gene_id "ENSG00000249396.1"; transcript_id "ENST00000515243.1"; gene_type "lincRNA"; gene_status "NOVEL"; gene_name "RP11-1C1.4"; transcript_type "lincRNA"; transcript_status "KNOWN"; transcript_name "RP11-1C1.4-001"; level 2; tag "basic"; havana_gene "OTTHUMG00000162051.1"; havana_transcript "OTTHUMT00000367039.1";

Thanks very much for your help.

Hi Francesca,

Try to use import() from the rtracklayer package instead of makeTxDbFromGFF(). The former imports everything from the file while the latter selectively imports only the information it needs to build a TxDb object.

H.