In another post, a guy wanted to know how to analyze paired-end data and use them to predict microRNAs.
I never heard about a paired-end protocol for miRNAseq and would be interested in some more information. Does anyone know this protocol?
My questions would be:
- Since the reads from mature miRNAs are very short, do the two pairs completely overlap with each other?
- Is this protocol still strand specific? Is the first mate always the one on the correct strand?
- I don't think that recent tools like miRDeep, or miRanalyzer can handle this information. Are there tools which can?
- ...
I would be really thankful for some input! :)