Filter a BED file based on genome coordinates for gene names
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3 months ago
joker • 0

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?

BED GTF GFF • 624 views
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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... ...

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

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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

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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.

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

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3 months ago

Via BEDOPS bedmap:

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