How I can find sequences
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5.9 years ago
hosin • 0

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 • 867 views
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5.9 years ago
h.mon 35k

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
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5.9 years ago
Tm ★ 1.1k

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

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