Bowtie Reference Sequence Cannot Contain N, But Can It Contain Other Nucleotide Variables?
I'm trying to use bowtie with my own index reference. The problem is my reference contains nucleotide variables like M, S, Y, K etc. In the manual it clearly states that it discard sequences with N, but says nothing about the other nucleotide variables stated above. Has anyone looked into this?
1 answer
check this post for ambiguous nucleotides in the reference: http://www.biostars.org/post/show/3507/mapping-to-genome-with-ambiguous-reference-characters-rykmsw-etc/
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