Alignment of reads in REPETITIVE regions

[fenguita]

Hi All

I am dealing with a smallRNA seq dataset from Ilumina machines in patients that showed trinucleotide expansions in some genes. Since this is a repetitive region that could be matched elsewhere in the genome, how can I deal with that ?.

I am using Bowtie for alingning the reads. When I use a very astringent approach (-m 1), I got no reads aligned with my region...

Any of you is dealing with something like that. Any suggestions for more specialized software do circunvent these problems ?

All the best and thanks in advance

Paco