Where can I download a BED file with exonic regions?

Question

[njornet]

Hello,

I'm going to perform adaptive sampling with ONT for enrichment of exonic regions. I've tried using UCSC's Table Browser with Group Genes and Gene Predictions and Track NCBI RefSeq and GENCODEV47, I've also tried using filters but I'm not sure how they work. From all the bed files I generated the percentage of covered genome is between 45 and 60% with is obviously not what I want. I've also taken into account that regions may overlap.

How can I download only the exomes?

Thank you.

[Pierre Lindenbaum]

From all the bed files I generated the percentage of covered genome is between 45 and 60% with is obviously not what I want.

how did you do that ? You must use bedtools merge to merge the exons from the transcripts of the same gene.

Answer 1

[ATpoint]

You can download the GTF file, for example from GENCODE, filter for type == "exon", collapse overlapping intervals and then use these coordinates as the exome.

For example:

gzip -cd gencode.v47.annotation.gtf.gz \
| awk '$1 !~ /^#/ && $3 == "exon" {print $1, $4, $5}' OFS='\t' \
| sort -k1,1 -k2,2n -k3,3n \
| bedtools merge -i - > exome.bed

[njornet]

That worked, thank you very much

[Pierre Lindenbaum]

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