Hello!

I am using HISAT to align RNA-seq reads against a reference genome with possible errors as INDELS and variations. The program runs fast and results looks pretty coherent but I find less alignment rate than using Tophat previously. I guess this is because I was using specific parameters open to indels and mismaches like this:

--read-mismaches 4 \ --read-gap-length 4\ --read-edit-dist 4 \

So, which are the proper parameters to set in new HISAT version?