Dear all,
STAR manual said set --sjdbOverhang at readlength-1. I am confused by this with two questions.

1. If I generated genome index by setting it at 100 previously, and now I have a PE150 reads, should I re-generate genome index by setting it at --sjdbOverhang 149?

2. If I use --clip3pNbases 50 during mapping, should I set --sjdbOverhang at 99 (is from: 150 -50 -1)?

Thanks for your help.
Best.
You know the manual says about sjdbOverhang

> **In most cases, a generic value of 100 will work as well as the ideal**
> **value.**

http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf

