mirdeeps number of replicates

Question

[kylvalda]

Hi,

trying to analyze miRNA-Seq data from 20 versus 20 biological replicates (cell types).

mirdeep2 mapper.pl works fine - I get mapped% output from each of the 40 files.

But feeding the resulting mapped reads.fa into quantifier.pl, it only takes into account the first 9 samples:

All the results.csv and .html and each miRNA.pdf only shows data from the first 9 samples.

I used

quantifier.pl -p hairpin.fa -m mature.fa -c hsa -y 010916 -r 010917_miRNA_mirdeep2_reads.fa

with or without -n -x -c doesn't make a difference.

Is there something I'm not aware of?

The documentation is not very detailed, so I'm a bit lost.

Cheers :-)