Hi, I have aligned some Solexa RNA-seq data to refseq mRNA sequences. The aligned location in the alignment report is relative to each refseq sequence start. Is it possible to map the aligned results back to genome with current available tools in Bioocnductor? In other words, I want to convert the alignment position relative to genome location. It is relatively easy for the exon sequences, but it is more complicated for the ones aligned to the splicing junction. I think this is doable in R, but I just want to check to see if there is already such a function avavilable. Thanks in advance.
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