I'm studying on a plant that has no reference genome and only has one scaffold assembly and one gff3 annotation file. Can I create an index with the same assembly and gff3 in STAR and do the mapping? If I want to do de novo assembly using the Galaxy Can I import the links of 20 fastq files from the RNA-seq of the samples together to construct the Reference Genome with Trinity? If this is possible, please help me import the links of these files together into Galaxy and make the reference genome.
Thanks a lot