How IUPAC ambiguity codes are represented in Burrows-Wheeler transform ?
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5.1 years ago
Fadel ▴ 20

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 :))

alignment indexing • 1.2k views
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5.1 years ago

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.

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Thanks @Vijay Lakhujani

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