Question: How I can find sequences
0
gravatar for hosein_salehi6
11 days 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 • 119 views
ADD COMMENTlink modified 11 days ago by toralmanvar420 • written 11 days ago by hosein_salehi60
1
gravatar for h.mon
11 days ago by
h.mon16k
Brazil
h.mon16k 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 11 days ago by h.mon16k
1
gravatar for toralmanvar
11 days ago by
toralmanvar420
toralmanvar420 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 11 days ago • written 11 days ago by toralmanvar420
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