As am not an expert in the field, Hence I could like to know few basic concept on how STAR generate Splice Junctions Database(sjdb/SJ.out.tab) while indexing the reference genome with gtf file.
I find information from STAR Manual: http://labshare.cshl.edu/shares/gingeraslab/www-data/dobin/STAR/STAR.posix/doc/STARmanual.pdf
Under session : 8.5 Splice Junctions Database
But couldn't able to understand how only with reference genome and GTF file, Splice junction file is constructed within the genome directory.
I really appreciate your valuable response in advance.