aligning using bowtie2?
I am doing aligning with bowtie2 and just need reads that aligned exactly 1 time. so I have performed 2 ways: but I am not sure whether the first one is correct or not, while most of literature used the second one?
1= bowtie2 --very-sensitive --score-min C,0,0 --> that number of aligned exactly 1 times increased but the overall aligning decreased.
2= bowtie2 --very-sensitive --> that number of aligned exactly 1 times are less than first way but the overall aligning is higher.
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See this post on how to extract unique alignments. There are plenty of questions on how to extract reads that map 1/2/n times. Use google and the search.
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