I used mirDeep2 for my analysis with the following command lines:
mapper.pl (without option q)
mapper.pl trimmed_data.fq -e -h -i -j -m -p bta.fa -s reads_collapsed.fa -t reads_vs_refdb.arf -v
miRDeep2.pl reads_collapsed.fa bta.fa reads_vs_refdb.arf mature_ref_bta.fa mature_other.fa hairpin_ref_bta.fa -t bta 2>report.log
Later I wanted to loosen my criteria to allow mismatches. I added option q when running mapper.pl and used the outputs, reads_collapsed_mismatches_allowed.fa and reads_vs_refdb_mismatches_allowed.arf, as inputs for miRDeep2.pl without changing any other parameters for miRDeep2.pl.
1. mapper.pl (with option q to allow mismatches)
mapper.pl trimmed_data.fq -e -h -i -j -m -p bta.fa -q -s reads_collapsed_mismatches_allowed.fa -t reads_vs_refdb_mismatches_allowed.arf -v
- miRDeep2.pl (same as the first run)
miRDeep2.pl reads_collapsed_mismatches_allowed.fa bta.fa reads_vs_refdb_mismatches_allowed.arf mature_ref_bta.fa mature_other.fa hairpin_ref_bta.fa -t bta 2>report.log
The number of reads mapped to reference genome bta.fa increased when option q was included. However, the results from miRDeep2.pl module are EXACTLY the same. I have tried these methods for different datasets and still see the same things: output from mapper.pl were different but output from miRDeep2.pl were the same even though the mapper.pl module was run differenlt. Please help me with the following questions:
- Why I allow mismatches mapper.pl with q option), but the results after miRDeep2.pl were the same?
- What can I do to allow mismatches in the miRNAs search?