I have small RNA-seq data avaliable for two samples (wt and mutant), each of which have three replicates. I mapped the small RNAs on genome, and next want to identify which transcripts produce significantly more small RNAs in wt relative to mutant. Do you think Cuffdiff, edgeR and DESeq are suitable for this job? Is it the same as mRNA-seq differential gene expression analysis?
Thank you very much for any of your suggestions or comments.