I am reading about Burrows-Wheeler transform and some tools which have adopted it like BWA and HISAT
and I couldn't figure out how different IUPAC ambiguity codes are represented in Burrows-Wheeler transform !
I highly appreciate if u guys can direct me to any articles dealing with this problem :))
I don't know about BWA but Bowtie 2 considers all ambiguous characters in the reference (including IUPAC nucleotide codes) to be Ns. Since, both uses BWT, the same might be true for BWA.
Thanks @Vijay Lakhujani
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