Question: How to get nucleotide sequences for a given list of genomic positions.
3
gravatar for Naresh D J
4.3 years ago by
Naresh D J80
Turku/BTK
Naresh D J80 wrote:

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 • 1.9k views
ADD COMMENTlink modified 4.3 years ago by Ming Tang2.6k • written 4.3 years ago by Naresh D J80
5
gravatar for Nicolas Rosewick
4.3 years ago by
Belgium, Brussels
Nicolas Rosewick9.0k wrote:

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

ADD COMMENTlink written 4.3 years ago by Nicolas Rosewick9.0k

Thank you. It is handy.

ADD REPLYlink written 4.3 years ago by Naresh D J80
2
gravatar for SP
4.3 years ago by
SP270
Germany
SP270 wrote:

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).

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by SP270
2
gravatar for EagleEye
4.3 years ago by
EagleEye6.7k
Sweden
EagleEye6.7k wrote:

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

ADD COMMENTlink modified 4.3 years ago • written 4.3 years ago by EagleEye6.7k
2
gravatar for Ming Tang
4.3 years ago by
Ming Tang2.6k
Houston/MD Anderson Cancer Center
Ming Tang2.6k wrote:

I have blog posts on this http://crazyhottommy.blogspot.com/2013/04/batch-converting-coordinates-to.html http://crazyhottommy.blogspot.com/2015/02/fetch-genomic-sequences-from-coordinates.html

ADD COMMENTlink written 4.3 years ago by Ming Tang2.6k
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