During my analysis of RNA-seq data regarding alternative splicing and splicing pattern, I came across some standard options of the STAR algorithm, which I could not quiet follow.
--alignSJoverhangMin 8 (minimum overhang for unannotated junctions) --alignSJDBoverhangMin 1 (minimum overhang for annotated junctions)
I have concerns using this standard options, which regulate the minimal overlap of a read over the exon junction. I don't understand why one nucleotide overlap is enough to map a read to an annotated exon junction. And why would you not generally use the same minimum overlaps for a junction to begin with?
So my question is, what would you use as an minimal overlap? Would you use the standard settings or for example 6nt for both junctions?