I'm working on an uncommon insect. There's a reference genome for it but the quality is not that good. I decided to use STAR 2-pass to get my data better mapped, but I'm not sure if I should choose "with re-generated genome" or "without re-generated genome". What's the difference, or a better question, what does it mean? The manual doesn't thoroughly illustrate this. Anyone has an idea about this? Thanks!
I think "with re-generated genome" is the way to go, if you have more than just one sample and some available gene annotations of the genome, so that the "re-generated genome" will be better annotated with exon junctions. However, I am not sure how much benefit you can get with a uncompleted reference. If the reference genome is still in pieces, I will tend to use Trinity to assemble the transcriptome first, but this is really depending on what you are looking for.
Definitely, you have to use "with re-generated genome" option. Alternatively, I think another way is to assemble RNA-Seq reads using Trinity to make a so-called 'genome-guided assembly', whereby reads are first aligned to the genome, partitioned according to locus, followed by de novo transcriptome assembly at each locus. You can create if necessary the transcript sequences using tophat/cufflinks
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