I am moving from bowtie to bwa, as bwa considers gap while doing mapping.
But i don't know how to get all the possible hits for a single read on the reference genome(besides the perfect one), like using -a with bowtie. I tried -N, but it does't work. Although X1 in the sam file can give me the number of suboptimal hits, I need the details of the hit like the optimal one.
Anyone can give me some clue, if bwa can't do this, what else can?
ok, I got the result myself, after .sai, using bwa samse -n INT to display maximum n match for each read
But i don't know how to get all the possible hits for a single read on the reference genome(besides the perfect one), like using -a with bowtie. I tried -N, but it does't work. Although X1 in the sam file can give me the number of suboptimal hits, I need the details of the hit like the optimal one.
Anyone can give me some clue, if bwa can't do this, what else can?
ok, I got the result myself, after .sai, using bwa samse -n INT to display maximum n match for each read
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