Hello all. Recently our core lab ran the Illumina small RNA protocol on a sample (human RNA) to collect miRNA sequence. The primary purpose is to analyze differential expression of the known miRNA species in the various samples run. It is now up to me to do the bioinformatics part. I know that I can get a set of known miRNA sequences from miRBASE. I also know that I will have to either mask or trim the adapter portion of the read prior to aligning. Can anyone who has done anything similar offer some advice? What tools do you think are best for the job? Should I be trying to align to just the miRNA sequences or the whole genome?
Thanks in advance.
Thanks in advance.
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