Hi all, now I have RNA sequencing data which belongs to 5 species (all in the same genus) and whole genome data for 1 species. Do you think I need to do de novo assembly or use the genome data as reference to assemble the transcriptome data? I am not sure if the reference sequence will make any bias on different species. If you have any experience, would you please share it? Many thanks in advance!
It is better to use a genome reference. Using de novo transcriptome assembly just makes sense if the species are not close related.
It's all dependent on your model and do you have a good reference genome. You can get this information easily and do some thinking over it. You will get a way.
Both methods are feasible. In my view, since all sequences are from the same species, first look for a reference genome and use reference based alignment then if you have more time you try denovo. If you fail to get a reference genome, then go straight to denovo but you need to get an appropriate assembler.
you can use both method..and then you can compare both assembly results by using BUSCO software and then you can may fid the best result. good luck