Hi,
As stated in the hisat2 manual, hisat2 reported multiple primary alignments when -k parameter was more than 1. The first print primary alignments was the first searched primary alignments, not primary alignments with the best alignment scores. I noticed that hisat2 can report all alignments through -a parameter. Are the first print primary alignments with -a parameter the best? If not, I wonder if I can use other parameters to find the best primary alignments.
Hi, As stated in the hisat2 manual, hisat2 reported multiple primary alignments when -k parameter was more than 1. The first print primary alignments was the first searched primary alignments, not primary alignments with the best alignment scores. I noticed that hisat2 can report all alignments through -a parameter. Are the first print primary alignments with -a parameter the best? If not, I wonder if I can use other parameters to find the best primary alignments.
Thanks for your help.