I have Illumina reads (36bp, single end) from mRNA sequencing of human samples in two different conditions. I want to find the probable effective simple sequence repeat (SSR) markers between experimental conditions. Since the genome is available, I mapped reads to the reference genome (global alignment) and extracted the consensus sequence from bam file. I considered the lowest level for insertion/deletion cost during mapping, please advise me another useful option for mapping to this end. However, the consensus sequence was full of N, referring no read mapped to that region. Could you please let me know if I should determine the SSR on this consensus sequence or you have alternative suggestions and comments for SSR discovering in RNA-seq data when a reference genome is available?