The RSEM software appears to require a reference sequence set (e.g. hg19) and a gene database (e.g. RefSeq). Could it be made more flexible so that the gene database is not required for the scenario where the reference sequence set is not a genome but a set of alleles of some highly polymorphic genes, hence it's the number of reads assigned to each of the alleles which is the quantity of interest?
The RSEM software appears to require a reference sequence set (e.g. hg19) and a gene database (e.g. RefSeq). Could it be made more flexible so that the gene database is not required for the scenario where the reference sequence set is not a genome but a set of alleles of some highly polymorphic genes, hence it's the number of reads assigned to each of the alleles which is the quantity of interest?