Bowtie Reference Sequence Cannot Contain N, But Can It Contain Other Nucleotide Variables?

Question

[diltsjeri]

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?

Answer 1

[Rm]

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/