Any tips? I know STAR aligner is optimised for mammalian alignments. I have a reference genome with a gff3 file for a plant and there are only details for exon, CDS, UTRs, but not introns. Additionally the genome is presented in scaffolds only, not chromosomes. The default STAR settings put max intron length to around 500,000 nt which is huge. Can anyone suggest a suitable maxintron value, or point me to literature on such a matter. It seems this goes unreported in alignment methodology most of the time.