retrieving sequences of a upstream and downstream of a coordinate for hg19

Question

[kanwarjag]

I have location of peak summit from my chipseq data and want to extract sequences 500 bp upstream and downstream of this coordinate from hg19. What should be easieast approach. Apology for a naive question, but I could not recollect or find on net how I used to do this.

Thanks

Answer 1

[ATpoint]

awk 'OFS="\t" {print $1, $2-500, $3+500}' summits.bed | samtools faidx hg19.fa /dev/stdin > sequences.fa