I am working on RNA-seq data for studying miRNA from porcine samples. I run miRDeep18.104.22.168 on ubuntu (under the bioconda environment). miRDeep2 took 3 hours to run and gave me the results with an error " RNAfold: invalid option -- n ".
when I look at the results, I got CSV, HTML, and bed formatted results. But the results folder generated by miRDeep2 was empty. The bed file is empty while the other two have results.
Can I take these results or I don't have to take it? any ideas on how to fix this?