Recently I have got some miRNA reads from the small RNA seq data. I have filtered them for quality and removed the adapters with FASTX. I want the align the reads to the miRbase by using SHRiMP.
- Which SHRiMP parameters should I consider while aligning the reads to miRBase?
- Which miRbase file mature/precursor file should I use as reference?
- In there a need to create an index for the reference miRBase file before aligning the miRNA reads to it?