Entering edit mode
6.9 years ago
nmauri
•
0
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?