I have some difficulties in understanding the option sjdbOverhang in STAR. This option is set when making use of a splice junctions database. The manual defines it to be: "the length of the donor/acceptor sequence on each side of the junctions, ideally = (mate_length - 1)". It seems to be a very important option, because if it is set to 0 (default), the splice junctions database is not used.
I don't think it's the minimal alignment length for a read spanning the junction, because there's already the option alignSJDBoverhangMin for that, which is defined as "the minimum overhang (i.e. block size) for annotated (sjdb) spliced alignments".
is it then the expected length maybe?