Question about parameters
Ben7124 opened this issue · 1 comments
Hello,
In practical usage, which parameters are best? Is mirgenedb preferred to mirbase? Do the "ai" and "trf" flags improve detection? Do you recommend the use of these flags?
Thank you!
There is no 100% right answer as it depends on what you want to learn, but I'll do my best. MirGeneDB is preferred over miRBase in almost every scenario. If you are looking for a biomarker and you don't care if it is a bonafide miRNA or not, miRBase might be useful. If you are interested in biology, then only MirGeneDB should be considered. The -ai flag gets very little useful data, so that is probably not that helpful. The -trf is good if you are also interested in tRF distributions in the data. They don't improve detection. The miREC method is good for curtailing a long tail of isomiRs, but comes at the cost of slowing down throughput through miRge.
tl;dr MirGeneDB >> miRBase; don't use -ai; use trf if interested in tRFs.