Question: GenomicFeatures makeTxDbFromGFF: Select by columns in gtf file
1
gravatar for User 7754
4.4 years ago by
User 7754230
United Kingdom
User 7754230 wrote:

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

 

genomicfeatures R • 2.8k views
ADD COMMENTlink modified 2.2 years ago by Biostar ♦♦ 20 • written 4.4 years ago by User 7754230

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

ADD REPLYlink modified 3 months ago by RamRS25k • written 4.4 years ago by cpad011212k
1
gravatar for User 7754
4.4 years ago by
User 7754230
United Kingdom
User 7754230 wrote:

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
ADD COMMENTlink modified 3 months ago by RamRS25k • written 4.4 years ago by User 7754230
2

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.

ADD REPLYlink written 4.4 years ago by cpad011212k
1

Thank you for your reply, I will try that!

ADD REPLYlink written 4.4 years ago by User 7754230
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