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@joemphilips(Joe Miyamoto)inビットバンク株式会社

fasta fileから特定の領域のみ抜き出す

Last updated at Posted at 2015-12-16

samtoolsのfaidxを使用する

samtools faidx <genome>  # まずはindexを付ける
samtools faidx <genome> <chromosome name>:<start>:<end>

例

常染色体のみ抜き出す

samtools faidx humanhg19.fa chr{1..23} > humanhg19_longcontigs_only.fa

1番染色体と2番染色体の一部のみ抜き出す

samtools faidx humanhg19.fa chr1 chr2:10000:20000
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