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How do I get the 3bp sequence on either side of a co-ordinate

Hi all,

After I generate BAM or SAM files from my data, and have the coordinates of the 5' end of each read, how can I get the 3bp sequence on either side of this co-ordinate (total 6bp sequence) from the reference genome?

sam genomics sequencing
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updated by Ram Ram • written by nrav58 • nrav58

1 answer

I recommend bedtools. Start by expanding your 5' coordinates by the 3bp.

bedtools slop -b 3 -i five_prime.bed -g my_genome.fa.fai > five_prime_window.bed

Then, get those sequences from your genome.

bedtools getfasta -fi my_genome.fa -bed five_prime_window.bed
• 0 views • link
updated by Ram Ram • written by Adam • Adam

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