Question: How I can find sequences
0
gravatar for hosein_salehi6
4 months 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 • 189 views
ADD COMMENTlink modified 4 months ago by toralmanvar650 • written 4 months ago by hosein_salehi60
1
gravatar for h.mon
4 months ago by
h.mon21k
Brazil
h.mon21k 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 4 months ago by h.mon21k
1
gravatar for toralmanvar
4 months ago by
toralmanvar650
toralmanvar650 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 4 months ago • written 4 months ago by toralmanvar650
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