Hello everyone, I working on some human samples, I have their mRNA and the miRNA dataset in triplicates. Now, I'm interested in studying the miRNA - Protein Coding Gene (PCG) interactions using these dataset. Hence, I used MiRanda, but the results which I get are more obscure.
In total, I have 10300 expressed PCG and 600 expressed miRNAs, and when I use MiRanda on these data, I get a target for every possible miRNA. (i.e. in the output file I have all the 600 miRNAs targeting 10290 PCGs). This shouldn't be true.
The MiRanda command which I used:
/media/tools/bin/miranda expressed_mirna.fasta expressed_protein.fasta -out miranda_output-1.fasta -quiet -strict
- Am I missing something in the MiRanda command?
- Why the results are being so obscure? there are many false positives in there.
If anyone can help me understand this. Thank you.