How to run quantifier from miRDeep2 (miRNA seqs from MirGeneDB)
Dear all,
I want to perform miRNA quantification using quantifier.pl from miRDeep2. As default miRDeep2 is compatible with miRBase but I have to perform the quantification with mature and precursor sequences (fasta format) of miRNAs from MirGeneDB. I ran the tool as below:
quantifier.pl -p pre_miRNAs.fa -m mature_miRNAs.fa -r reads.fa
I do not get the expected output. I get these messages:
0 mature mappings to precursors
and
Warning: 0 mature sequences mapped to any of your given precursor sequences
The output file miRNAs_expressed_all_samples_1691413314.csv is empty considering that I have the mapping of my reads to provided miRNA sequences. I also do find mature sequences in precursor sequences when I search them using the grep function in bash.
Could someone please help me to solve the problem? Thank you.
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I solved this issue. The reason was that the precursor IDs did not match the mature IDs so I removed the "_pre" and the script worked as expected.