we're looking for a tool for Hierarchical mapping. Is there something like that out there? With Hierarchical I mean, i would like to start the mapping process with specific parameters and than iterate over the unmapped reads with increasing permissiveness (decreasing stringency). We mainly would like to better control the number of allowed mismatches and their allowed position in the reads. and the number of multi-mapped reads
The reason for this analysis is a data set of very shirt reads (~30-50nt), which have due to their biology high similarity. Due to the sequencing procedure we know that the used RT can cause mis-incorporations in specific positions, we would like to control for. Due to the high similarity of the reads we might get a lot of multi-mapped reads, which can differs only in one or two bases. This can cause problem in mapping those reads. We therefor would like to start very stringent and than re-run the mapping with different parameters, which can increase the results.
Does anyone know of a tool that can do this kind of analysis?
thanks in advance for any suggestions