GenomicFeatures makeTxDbFromGFF: Select by columns in gtf file
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
1 answer
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
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Could you please paste 3-4 lines from your gtf file here?