Building STAR Genome Index for nanopore RNA sequencing 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.

Running 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?
The parameter is used to determine how much sequence STAR indexes on each side of a splice junction to improve its alignment accuracy.  For very long reads, this may not be ideal. I am not sure if STAR is capable of including multiple splice junctions since a long read is more than likely to span more than one.  

It may be worthwhile to consider aligning your reads directly to transcripts and taking the reads that align poorly and using them to look for novel transcripts.