Hello everyone! I have a trouble mapping the reads to a extremely tiny reference using bowtie/bowtie2. I have a mass of sequencing data (PE150),and I only want to focus 20 bp of the each 150 sequence, but I don't know the accurate location of the 20 bp need to notice in each sequence because of mutation and indel. At the same time, I have a expected library containing all possible sequences of the 20bp. So I want to use the expected library of the 20bp to build a reference,then mapping the reads to the constructed reference. Even I try many combinations of parameters,I didn't find the matched 20 bp sequence as the reference is too small. If you have any suggestions, please let me know .Thank you a lot.