Filter a BED file based on genome coordinates for gene names

Question

[joker]

Hi, I have BED file with certain regions of interests that looks like this:

chr1 0 91923
chr1 323234 4596845
..

with the start and end coordinates for each gene for the respective chromosome.

But I want to include maybe the gene name, since I need them for my downstream analyses. I have the GTF file for the whole genome with the annotations (gene names, start/end coordinates).

How can I use this GTF file to add the gene names to the bed file? I thought of using bedtools intersect, but not sure how to do this. Maybe: bedtools intersect -a input.bed -b input.gtf > output.bed?

But how is bedtools intersect aware of the column specific format of the GTF file? Or might there be also a way to filter the GTF file based on the coordinates in the BED file?

[Pierre Lindenbaum]

convert GTF to bed before calling bedtools intersect : How To Convert Gencode Gtf Into Bed Format ? ; How to convert gtf to bed format ; Converting gtf format to bed format ; etc... ...

[joker]

Hi, thanks! Is there also a way to filter the GTF file to include the records based on the BED file coordinates?

[GenoMax]

You may want to check out AGAT toolkit. Here is one promising option (not BED) but may work: https://agat.readthedocs.io/en/latest/tools/agat_sp_filter_feature_from_keep_list.html

[joker]

I am already aware of the AGAT toolkit. But the script you mentioned only takes a gff/gtf file and a list of genes as inputs and extracts the overlaps based on the provided list.

But in my case I don't have the gene names, only the coordinates in bed format as mentioned before.

[Pierre Lindenbaum]

but you can use bedtools intersect with a gtf and a bed

Answer 1

[Alex Reynolds]

Via BEDOPS bedmap:

bedmap --echo --echo-map-id-uniq regions.bed <(gtf2bed --attribute-key=gene_name < annotations.gtf | awk ($8=="gene")) > answer.bed

• https://bedops.readthedocs.io/en/latest/content/reference/statistics/bedmap.html
• https://bedops.readthedocs.io/en/latest/content/reference/file-management/conversion/gtf2bed.html