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Hi All,
Is there any software which can map reads to IUB coded reference for SOLiD data? The reason I am looking for this tools is..we have a data from SOLiD which is similar to bisulfite treated sequencing...where random Cs are converted to Ts which only few % of the genome(~10-15%)...we want to map these reads to the ref but want to make sure that no mismatch penalty is applicable when converted Cs(T) map to ref seq...
Is there any software which can map reads to IUB coded reference for SOLiD data? The reason I am looking for this tools is..we have a data from SOLiD which is similar to bisulfite treated sequencing...where random Cs are converted to Ts which only few % of the genome(~10-15%)...we want to map these reads to the ref but want to make sure that no mismatch penalty is applicable when converted Cs(T) map to ref seq...