GenomicFeatures makeTxDbFromGFF: Select by columns in gtf file

Question

[User 7754]

Hi,

I am trying to create a function to extract the promoter regions from a gtf file only for "lincRNA" and "antisense" (under "type" column in the gtf file).

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

library("GenomicFeatures")
txdb = makeTxDbFromGFF("file.gtf", format="gtf")

But I don't think the column in the gtf file called "type" was imported.

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

(Then I think would need to select only the exons and then the regions up and downstream by gene (which I think is done by the function "promoters" in GenomicRanges))

Thank you

[cpad0112]

Could you please paste 3-4 lines from your gtf file here?

Answer 1

[User 7754]

Yes of course, the gtf 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
1       pseudogene      gene    11869   14412   .       +       .       gene_id "ENSG00000223972"; gene_name "DDX11L1"; gene_source "ensembl_havana"; gene_biotype "pseudogene";
1       processed_transcript    transcript      11869   14409   .       +       .       gene_id "ENSG00000223972"; transcript_id "ENST00000456328"; gene_name "DDX11L1"; gene_source "ensembl_havana

[cpad0112]

I tried with above example and no luck for me either. But one thing you can also consider is to convert gff to sqlite (if there are no other answers) and load it. txdb object is basically sqlite object.

[User 7754]

Thank you for your reply, I will try that!