I am newbie to linux and NGS. Can anyone help me out how to get information about splice junctions using HISAT2?

The command I'm using is giving information in single file about alignment in SAM format. The command is as follows:

    ./hisat2 -p 64 --max-intronlen 10000 -x /data/memona/hisat2-2.1.0/hisat_index -1 /data/memona/SRR959590_A_1P.fq -2 /data/memona/SRR959590_A_2P.fq -S /data/memona/results/hisat_align.sam &
Hi blooming.daisy333,

It is explained in the [manual][1]. You have to use the option --novel-splicesite-outfile.  
**Update:**  
<strike>Be careful there is an error how left splice sites are reported as I mentioned [here][2]</strike>  
 The splice sites are correctly reported but the format they use is not necessarily straightforward.


  [1]: https://ccb.jhu.edu/software/hisat2/manual.shtml
  [2]: https://github.com/infphilo/hisat2/issues/164