I've recently switched from using TopHat to using HISAT. Trying to figure out which parameters do what I want has been a bit of a challenge in spite of the manual. I realize some things may not be explainable as they are proprietary. But I think a few of my questions can be addressed.
- Is there a "Mean Inner Distance between Mate Pairs" (TopHat) equivalent in HISAT?
- Is there a way to only display/align reads that have no mismatches? (I think I figured this one out, but see the next question)
- How does HISAT calculate the Alignment Score (AS)? From what I can tell with my data, if the read is a perfect match the AS = 0, but if there is a mismatch/insertion/deletion/soft-clipping/etc. it is around AS=250.
- How does the program decide if it is using HGM or HGFM?
Thanks for any help that can be provided!