Dear all, I want to use the STAR alignment tool available in usegalaxy.org, i know that the default parameters are optimized for mammalian genomes, in my case it's for plant genomes, particularly for legumes. So which parameter i should to change, in my alignment? I know that the intron size is an important issue because the introns in plants are smaller than mammalians, so I will use it between 60 and 6000 according to what was described for splicing in Arabidopsis, but there are any other parameter that i have to change. Thanks for your attention.
STAR worked very well for me on hundreds of plant transcriptomes across about 10 species.
I used 2pass mode instead of integrating the annotation, as non-arabidopsis annotation tends to be fairly poor, especially for lowly expressed transcripts.
Otherwise the intron size parameter was fairly key as you say. Browse your genome and or use Bedtools to check the annotation of your genome in order to empirically determine intron size.