I am aligning a dataset of 1,000,000 reads oh human mRNA sequenced on Oxford Nanopore Technologies' MinION, and would like to use the STAR aligner, using the parameters recommended by Pacific Biosciences for long reads.
According to this Google Groups thread, in setting up the genome index for short reads, the parameter
sjdbOverhang should be set to 1 less than the read length. Obviously, with long (mean 1.7Kb, max >50Kb) reads, this doesn't make sense.
STARlong --runMode genomeGenerate without setting
sjdbOverhang sets the parameter to
0. Does anyone know what this means, how it might affect mapping, and what I should set it to for my long reads?