HISAT2是一款用于“对应（map）”二代测序数据（全基因组、转录组和外显子组）至目标基因组的工具，用来替代HISAT和TopHat2。本文汇集一些使用HISAT2的常见问题问答。
一个常见的双端测序样本HISAT2输出统计：
10000 reads; of these:
10000 (100.00%) were paired; of these:
650 (6.50%) aligned concordantly 0 times
8823 (88.23%) aligned concordantly exactly 1 time
527 (5.27%) aligned concordantly >1 times
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650 pairs aligned concordantly 0 times; of these:
34 (5.23%) aligned discordantly 1 time
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616 pairs aligned 0 times concordantly or discordantly; of these:
1232 mates make up the pairs; of these:
660 (53.57%) aligned 0 times
571 (46.35%) aligned exactly 1 time
1 (0.08%) aligned >1 times
96.70% overall alignment rate
总共10000对reads；
8823对concordant pairs（一对既方向匹配又有合适距离的reads）有1次精确比对；527对concordant pairs有1次以上比对；34对disconcordant pairs;
616对不是concordant pairs，也不是disconcordant pairs中，571个reads有1次精确比对；1个read有1次以上比对；660个reads没有比对成功。
因此，整体比对率为1 - (660 / 2) / 10000
需要。
2016年9月10日