I have RNA-seq data generated by Illumina Hiseq 2000 as 100bp, PE from human, control and diseased samples. I'm looking for polymorphic simple sequence marker (SSR) between two groups of control and disease. I'm going to do genome-guided transcriptome assembly for each group, then survey the probable polymorphic marker between them. For genome-guided transcriptome assembly, I know about cufflinks and stringtie, but as I found here some people suggested to avoid using them. Could you please kindly suggest me the appropriate tool for this purpose?
Any other comments on the issue would be highly appreciated.