Question: How I can find sequences
0
gravatar for hosein_salehi6
10 weeks ago by
hosein_salehi60 wrote:

I have some coordinates ( like: chr24:40902129-41709809, chr25:11035146-11097889) from Ovis aries:Oar_v4.0 file. How I can find sequences for them. Thanks

sequence • 173 views
ADD COMMENTlink modified 10 weeks ago by toralmanvar530 • written 10 weeks ago by hosein_salehi60
1
gravatar for h.mon
10 weeks ago by
h.mon19k
Brazil
h.mon19k wrote:

There are a number of possibilities. For example, download and index the whole genome, and use samtools to extract regions of interest:

samtools faidx genome.fa
samtools faidx genome.fa chr24:40902129-41709809 > region1.fa
ADD COMMENTlink written 10 weeks ago by h.mon19k
1
gravatar for toralmanvar
10 weeks ago by
toralmanvar530
toralmanvar530 wrote:

If you have bed/gff file of coordinates, then you can use bedtools getfasta and if you have just couple of coordinates to extract the you can try seqkit faidx which is similar to samtools faidx

ADD COMMENTlink modified 10 weeks ago • written 10 weeks ago by toralmanvar530
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