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Mapping to reference with IUB codes

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  • Mapping to reference with IUB codes

    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...