I wonder if somebody knows how many different (not concatenated) samples can be analyzed with miRDeep.pl module of mirdeep2 package. I have some troubles to analyze more than 2 samples. After preparing reads_collapsed.fa (-m option to collapse reads applied) e reads_vs_genome.arf applying config-file e mapper.pl module for 12 samples, I've got an error running miRDeep.pl: repeated sequencies in the reads_collapsed.fa.

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The sequence
TGTAAACATCCTCGACTGGA
occures at least twice in sample XXX in your reads file
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Why does it happen? Did the collapsing failed?