生信基础概念之unique reads VS multi-mapping reads

Posted 2020-09-26 一周一paper，一周一技术

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