How to quantify novel microRNA read counts for each sample from miRDeep2

Question

[sri.dewi]

Hi,

I am wondering is there any way to extract read counts for each sample for novel microRNA predicted by miRDeep2. I could only find in the expressed_all_samples.csv file read counts for each sample for the known microRNAs but not for the novel ones. Did I missing something here? Thanks in advance for any kind of hint or help!

best, Dewi

Answer 1

[zarskili]

One method would be to first identify all the known and novel microRNAs in all of your samples pooled together (use the -d option with mapper.pl; and then use this output to run mirdeep2).

Next, create your own reference files using the novel and known miRNAs present in your samples. Then, you can run quantifier.pl for each sample using your custom reference fasta files rather than the miRbase ones.

I am not sure the best way yet to create the custom reference files.