# 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?

• Not an answer, but for full-length transcripts, it is worth considering traditional cDNA mappers such as gmap and blat. How well they perform highly depends on the error rate. They are probably ok at ~5% error rate. If you are using the older chemistry, they may not work, though. – user172818 Jun 7 '17 at 12:07
• A very good point. We're using GMAP as our baseline aligner, but I wanted to try out STAR to confirm the rather surprising results in this bioRxiv preprint: biorxiv.org/content/early/2017/04/11/126656 – Scott Gigante Jun 8 '17 at 2:05

I've found the STAR manual to be incredibly helpful with trying to navigate my way round all the STAR command line parameters. Here's the section on the sjdbOverhang parameter:
--sjdbOverhang specifies the length of the genomic sequence around the annotated junction to be used in constructing the splice junctions database. Ideally, this length should be equal to the ReadLength-1, where ReadLength is the length of the reads. For instance, for Illumina 2x100b paired-end reads, the ideal value is 100-1=99. In case of reads of varying length, the ideal value is max(ReadLength)-1. In most cases, the default value of 100 will work as well as the ideal value.