Dear forum, I would like to review a set of ~ 50 human RNA primer pairs (in fasta) on a genome browser. Their size range from 18 to 25nt. Some of them overlap splicing junctions. I have tried two approaches:
- blast on refseq RNA: fine but need a conversion to grch37 assembly (allowing split of the query over both side of splice junction)
- HiSat2 alignment: many are not found, I don't get why. (parameter L was set to 14, lower than min query length by 4nt).
I'm sure there is a simple solution as my objective is I guess not very original, but I don't find out. Do you have any guidance for generating a bed file fitting my needs? Thanks, Manu