I would like to analyze a set of miRNA data by suing miRDeep2. I have three samples and each has two replicates.
I managed to find out novel and known miRNAs by using config.txt in mapper.pl command line like this: mapper.pl config.txt -d -c -i -j -l 18 -m -p genome_index -s reads.fa -t reads_vs_genome.arf So I had one reads.fa and one reads_vs_genome.arf, then I used miRDeep2.pl.
Now I would like to find expression of miRNA in each sample to compare expression of each miRNA in different samples. Should I use miRDeep2.pl for each sample and its replicate separately or there are other ways. I know miRDeep2 pipeline but I don't know how I can mange expression analysis of multiple samples with this tool.
Thank you in advance.