searching the STAR manual for default STAR arguments, I stumbled upon the argument
--twopassMode. In my understanding, if you call it with
--twopassMode Basic, STAR takes all exon junctions from the first run with a given sample and uses it as annotated junctions in a second step of mapping of the same sample, which apparently leads to an increase in reads for not annotated exon junctions but the same number of novel found junctions.
I have RNA-Seq data of biological groups, four times each and am analysing the data for alternative splicing. Therefore I would like to treat annotated an not annotated splice sites as free from any bias as possible. Would you recomend using the
--twopassMode Basic or
--twopassMode None and what is the default value for STAR 2.5.4b?
Edit: The default setting in STAR is