I have sequenced reads from bovine miRNA (single end, raw reads 51bp). I have two groups. Each group with 4 repeats.
GroupA (GroupA_1, GroupA_2, GroupA_3, GroupA_4)
GroupB (GroupB_1, GroupB_2, GroupB_3, GroupB_4)
After trimming, I retained the reads with length 18-35 bases. My aim is to identify differential miRNA expression profiles.
Do I have to compared sequenced miRNA reads against bovine miRNA from miRBase mature.fa sequence or entire bovine genome?
Then planning to use htseq-count to compute the counts for Bovine miRNAs.