bowtie

最后发布时间 : 2023-08-06 19:44:18 浏览量 :

基本命令

bowtie-build ref1.fa bowtie/ref1.fa
bowtie bowtie/ref1.fa  reads_1.fq -S
bowtie bowtie/ref1.fa -1 reads_1.fq -2 reads_2.fq -S

关键的参数

Alignment：

-v：report end-to-end hits w/ <=v mismatches; ignore qualities or
-n：max mismatches in seed (can be 0-3, default: -n 2)（在seed region）
-l/--seedlen：seed length for -n (default: 28)(比对miRNA时调小)
-I/--minins：minimum insert size for paired-end alignment (default: 0)
-X/--maxins：maximum insert size for paired-end alignment (default: 250)（reads1和reads2头对头的距离，双端150时比不上）
Reporting:
-k：report up to good alignments per read (default: 1)
-a/--all：report all alignments per read (much slower than low -k)
-m：suppress all alignments if > exist (def: no limit)
--best：hits guaranteed best stratum; ties broken by quality