unique reads:在参考组上只有一个匹配点
multi-mapping reads:在参考组上有多个匹配点
下面是tophat的一个结果案例：
Reads: Input : 26140314 Mapped : 25159791 (96.2% of input) of these: 1027691 ( 4.1%) have multiple alignments (1832 have >20) 96.2% overall read mapping rate.
the quantity of unique reads ：25159791-1027691=
the quantity of multi-mapping reads：1027691
1027691个multi-mapping reads 产生了多少个alignment？或者提起unique reads用于下步分析？
$samtools view accepted.bam|grep -v ‘NH:i:1‘|wc -l
$samtolls view accepted.bam|grep ‘\bNH:i:1\b‘>accepted_unique.sam
生信基础概念之unique reads VS multi-mapping reads
原文：http://www.cnblogs.com/timeisbiggestboss/p/7099571.html