I have a non-coding RNA list with positions which is from mouse MTA microarray. What I am planning to do are 1. find their nearby genes, 2. find overlap miRNA.
I am trying to parse related tables/files from UCSC genome browser.
For gene annotation, I downloaded refFlat.txt.gz and knownGene.txt.gz. Which is better? Which one contains all genes annotation of mouse?
For miRNA, which file I should use?