I have total RNA-seq sequencing (ribosomal RNA depleted) of single end 49bp stranded RNA from mouse. From total RNA there is these subclasses: mRNA, polyA RNA, polysomal RNA, tRNA, ribosomal RNA (removed), lincRNA, miRNA, piRNA, siRNA, SRP RNA, tmRNA, snRNA, snoRNA, SmY RNA, scaRNA, gRNA, aRNA, crRNA, tasiRNA, rasiRNA, 7SK RNA.
My question is given miRNA is 20-24 nt and I have 49 bp RNA sequencing, I shouldn't have miRNA in my sequencing data as the size (nt length) is too small to be captured? Isn't a separate sequencing protocol needed if want the miRNA data from such an experiment?
I have gone down the route of: hisat2 -> featurecounts -> DESeq2 to perform differential expression using this data set. Anyone see a problem with the workflow that I used given mouse has a good genome and annotation to use.