miRDeep2 on Helix
miRDeep2 is a completely overhauled tool which discovers microRNA genes by analyzing sequenced RNAs. The tool reports known and hundreds of novel microRNAs with high accuracy in seven species representing the major animal clades. The low consumption of time and memory combined with user-friendly interactive graphic output makes miRDeep2 accessible for straightforward application in current reasearch.
Programs location
/usr/local/apps/mirdeep2/current
The environment variable(s) need to be set properly first. The easiest way to do this is by using the modules commands as in the example below.
$ module avail mirdeep2 ----------------------------- /usr/local/Modules/3.2.9/modulefiles -------------------------- mirdeep2/2.0.0.5 $ module load mirdeep2 $ module list Currently Loaded Modulefiles: 1) mirdeep2/2.0.0.5
$ module unload mirdeep2 $ module load mirdeep2/2.0.0.5 $ module show mirdeep2 ------------------------------------------------------------------- /usr/local/Modules/3.2.9/modulefiles/mirdeep2/2.0.0.5: module-whatis Sets up mirdeep 2.0.0.5 prepend-path PATH /usr/local/apps/mirdeep2/2.0.0.5 prepend-path PATH /usr/local/apps/bowtie/0.12.9 prepend-path PATH /usr/local/apps/viennarna/current/bin prepend-path PATH /usr/local/randfold-2.0/bin -------------------------------------------------------------------
How To Use
The following example can be copied from /usr/local/apps/mirdeep2/2.0.0.5/TUTORIAL . Then follow instruction in the 'TUTORIAL' file in this directory.
Example
% mkdir /data/$USER/Dir1; cd /data/$USER/Dir1 $ cp -r /usr/local/apps/mirdeep2/2.0.0.5/tutorial_dir . $ bowtie-build cel_cluster.fa cel_cluster $ mapper.pl reads.fa -c -j -k TCGTATGCCGTCTTCTGCTTGT \ -l 18 -m -p cel_cluster -s reads_collapsed.fa -t reads_collapsed_vs_genome.arf -v $ quantifier.pl -p precursors_ref_this_species.fa -m mature_ref_this_species.fa \ -r reads_collapsed.fa -t cel -y 16_19 $ miRDeep2.pl reads_collapsed.fa cel_cluster.fa reads_collapsed_vs_genome.arf \ mature_ref_this_species.fa mature_ref_other_species.fa precursors_ref_this \ _species.fa -t C.elegans 2> report.log
