miRCat2 Setup and Run

miRCat2 Setup and Run

Setting up miRCat2 requires the user to tell the software where to place the output using the menu -> set output directory.

The user must then configure the  required parameters for this run. Two defaults (plants and animals) are available using the checkboxes and a short description of each parameter is given below


  • repeats : maximum number of genome hits (default 25)
  • complex: complexity of sequence i.e. the sequence should not be represented in proportion of 90% only by one nucleotide or a combination of only 2 nucleotides (default 0.90)
  • randfold: if randfold should be performed (default false)
  • pVal: cut-off value if randfold param is true (default 0.5)
  • minLen: minimum length of the miRNA (default 20)
  • maxLen: maximum length of the miRNA (default 24 in animals, 23 in plants)
  • minFoldLen: minimum length of the miRNA precursor (default 40 in animals, 45 in plants)
  • maxFoldLen: maximum length of the miRNA precursor (default 100 animals, 250 plants)
  • maxAmfe: maximum adjusted MFE per 100 nt (default -22)
  • gapsInMirna: maximum number of consecutive gaps in the fold on the miRNA/miRNA* position (default 4)
  • allowComplexLoop: allows multiple bulks in the loop area on the fold (default false in animals, true in plants)
  • noLoops: maximum number of bulks to be allowed in the loop area on the fold, if the allowComplexLoop parameter is true (default 3)
  • clearCutPercent: percent of incident reads that should fall between the same start and end positions as the miRNA (default 0.95 in animals, 0.92 in plant)

After setup is complete the user can press the continue workflow button to initiate the miRCat2 run

A suite of tools for analysing micro RNA and other small RNA data from High-Throughput Sequencing devices