I am mapping illumina reads using bowtie/bwa to a reference genome with ambiguous reference characters (N, -, R, Y,K,M,S,W etc.).
For example: At a particular location where ambiguous reference character exists (R), I want read with either A or G to be matched as perfect match.
In the below case using bowtie, read is not able to match to the reference.
Reference: ATTCAAGCCCMGAGCGTMTATAAKGGAAGCTKCGCGTGTGTATGCATCAATTGGCAAGATGTTGTG Read:
Can you suggest options to set within bowtie/bwa or suggest other alignment tool where I can acheive this.
I learnt that "Alignments involving one or more ambiguous reference characters (N, -, R, Y, etc.) are considered invalid by Bowtie."