Recently we sequenced small RNA sequencing using Rapid Run platform. As the size of the small RNA ranges between 18 to 35bases. The reads from this run would have bases sequenced from the adapters and primers. I am planning to trim off the adapters and primers.
Step1: Trimming the adapters from reads generated
Step2: Aligning the reads against miRBase database using Bowtie2 tool.
I noticed that in miRBase all mature.fasta file has U base instead of T. But my reads have base T in them. how do I change the base U to T in mature.fa file in order to do alignment?
Do I need to compare against all mature microRNA sequences or just one species?