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.
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.