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How to get nucleotide sequences for a given list of genomic positions.

Hi, I have a text file of 7500 genomic positions with their chr, start, end and want to get their nucleotide sequences. Can someone point me some tool or any thoughts on how to do it?

Thank you,

chip-seq sequence ngs
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updated by Ming Tommy Tang Ming Tommy Tang • written by Naresh D J • Naresh D J

4 answers

Use getfasta from bedtools : http://bedtools.readthedocs.io/en/latest/content/tools/getfasta.html

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written by Nicolas Rosewick Nicolas Rosewick

if you use python:

    import pysam
    genome = pysam.Fastafile(path_to_genome+'genome.fa')
    sequence = genome.fetch(chr, start, end)

path_to_genome: would be any genome you have downloaded (e.g. hg19).

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written by SP SP

A: Retrieve a subset of FASTA from large multi-FASTA file

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written by EagleEye EagleEye

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