Running HISAT2

Running HISAT2

Reporting
The reporting mode governs how many alignments HISAT2 looks for, and how to report them.

In general, when we say that a read has an alignment, we mean that it has a valid alignment. When we say that a read has multiple alignments, we mean that it has multiple alignments that are valid and distinct from one another.

By default, HISAT2 may soft-clip reads near their 5' and 3' ends. Users can control this behavior by setting different penalties for soft-clipping (--sp) or by disallowing soft-clipping ([--no-softclip]).
报告成功比对包含了hisat2如何看待比对成功，以及如何报告他们。
hisat2说一个比对就是说一个read严格的比对到了基因组的一个位置，多个比对就是说一个read比对到了多个位置，并且这些位置彼此不同。默认情况下，hisat2对35端的要求不严格。用户可以通过设置soft-clipping（--sp）的不同处罚或禁止软剪切（[--no-softclip]）来控制此行为。

Distinct alignments map a read to different places
一个read被比对到了不同的位置
Two alignments for the same individual read are "distinc