I am trying to use augustus for gene prediction of a non model organism and currently looking at this link.
They have used blat for alignment to generate "hint" file but since I already have transciptome data on Illumina, I want to first generate a bam file (may be by using bowtie) and then convert it to wig file (as per the tutorial)
Is there any alternative approach for gene prediction in such cases? Any link to tutorial, tool or pointers will be highly appreciated. I am quite flexible with the approach/tool/method.