轉錄組數據比對，選用了hisat2，比對之后發現結果不太懂，于是整理了這篇筆記與大家分享，歡迎交流。

此處是一個轉錄組數據hisat2比對結果，bowtie結果也是這個格式。

17968900 reads; of these:    #reads數目
  17968900 (100.00%) were paired; of these:   #能配對的reads，由于用的是trimmomatic后的paired clean data，故100%
    4434269 (24.68%) aligned concordantly 0 times    #不能比對到基因組上
    10748474 (59.82%) aligned concordantly exactly 1 time   #比對到基因組上，且唯一匹配，即unique map
    2786157 (15.51%) aligned concordantly >1 times  #比對到基因組上，但結果>1次，即不唯一匹配
    ----
    4434269 pairs aligned concordantly 0 times; of these:  #上述不能比對上的reads中
      269467 (6.08%) aligned discordantly 1 time #這些雖然比對上了，但是不合理，例如方向、R1 R2之間的距離等
    ----
    4164802 pairs aligned 0 times concordantly or discordantly; of these:   #剩余的不匹配reads中
      8329604 mates make up the pairs; of these:
        5311882 (63.77%) aligned 0 times
        2073153 (24.89%) aligned exactly 1 time   #作為單端來比對，這些可以唯一比對
        944569 (11.34%) aligned >1 times   #這些不唯一比對
85.22% overall alignment rate  #結果是唯一比對+不唯一比對+不能比對中可以單端比對的

要看到，所謂唯一比對，可以直接從這個報告中計算。

referrence:
https://www.cnblogs.com/leezx/p/8540862.html
https://blog.csdn.net/weixin_30935137/article/details/86530092