I'm using miRDeep2 in order to detect and quantify miRNA in smallRNA-seq data. I'm getting some trouble with the quantification module. I use mice data and the hairpin.fa and mature.fa files from miRbase (v21). When I run the quantifier module with this command line:
quantifier.pl -p hairpin_ATCGN.fa -m mature_ATCGN.fa -r reads.fa -t mmu
I got this error
Error: No entrys for species "mmu or mmu" found in file hairpin_ATGCN.fa Please make sure that the given species argument matches the species id in your file hairpin.fa or say none
I already removed line containing non [ATCGNactgn] characters. When I do
grep "mmu" hairpin_ATGCN.fa
I got many lines like this:
I don't understand where is the problem with my files.
I also checked my mature_ATGCN.fa file and got:
Does anyone already solve this problem?
Thank you for your help