Hello,
I would like to clarify something related to the above conversation. I am running STAR 2.5.3a. My initial STAR run (I believe this is the indexing stage) was with --sjdbOverhang 100, and I am later running another tool called zUMIs which calls STAR. zUMIs asks for reads length, which in my case is 50 BPs. I assume zUMIs passed this on to STAR, which resulted in this error:
EXITING because of fatal PARAMETERS error: present --sjdbOverhang=49 is not equal to the value at the genome generation step =100
If I understand correctly, my options right now are:
- running STAR indexing again using --sjdbOverhang 49 and then trying zUMIs with 50 BP as I did before
- running STAR indexing without a GTF file at all, and this would prevent the error?
part of my problem is that I am not sure if zUMIs would be OK with me giving a larger number, lets say 100 as BP lengh, as it might use this later for something else.
Thank you,
Tom Snir.