I have some confusion here that would be great if you could clarify: Supposed I have a large set of scaffold in fasta format (from a genome assembly for example, and it may contain assembly errors), and I have a small reference cDNA set (obtained from Ensembl, so it can be considered as high quality reference). Normally, I was told that the larger set should be the subject for BLAST-ing and the smaller one should be used as query. Thus, should I makeblastdb of my large scaffold set and query the reference cDNA set against it? or doing vice-versa? (I have the feeling that using ref cDNA set as query is quite counter-intuitive because its role is for reference, so it should be the subject for BLAST-ing, isn't it?)
Thank you very much for any suggestion and clarification!