生信基礎概念之unique reads VS multi-mapping reads

unique reads:在參考組上只有一個匹配點

multi-mapping reads:在參考組上有多個匹配點

下面是tophat的一個結果案例：

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個multi-mapping reads 產生了多少個alignment？或者提起unique reads用於下步分析？

$samtools view accepted.bam|grep -v 'NH:i:1'|wc -l
$samtolls view accepted.bam|grep '\bNH:i:1\b'>accepted_unique.sam