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Performs novel miRNA discovery using miRanalyzer or mirDeep2, depending on what is installed and what you want to use. This was made to take the unmapped output files of the Align function as input.

It is recommended that all fasta sequences and bowtie index come from the same genome build and version. Requires miRanalyzer and FASTX-Toolkit to be installed.

Version 1.0
Bundle sequencing
Categories Novel smallRNA
Specialties generic
Authors Katherine Icay (katherine.icay@helsinki.fi)
Issue tracker View/Report issues
Source files component.xml function.scala
Usage Example with default values

Type parameters (generics)


Name Type Mandatory Description
fqFiles CSV Mandatory List of fastq files containing reads mapped to the genome but not mapped to any known miRNAs.
mirDP_genome FASTA Optional Input for miRDeep2. Fasta file of reference genome. Path should contain the Bowtie index files of the same file name. For example, "genome.fa" should abe in the same folder as "genome.[1-4].ebwt"
mirDP_mature FASTA Optional Input for miRDeep2. Fasta file of known mature miRNAs in reference genome.
mirDP_related_mature FASTA Optional Input for miRDeep2. Fasta file of known mature miRNAs of a related species. e.g. mouse or monkey for sequenced human reads.
mirDP_precursor FASTA Optional Input for miRDeep2. Fasta file of known miRNA transcripts (hairpin sequences).


Name Type Description
array Array<BinaryFile> Array of miRDeep2 results.


Name Type Default Description
Qscore string "-Q64" Quality score type of input fastq sequence. Values are either Sanger quality/Phred values '-Q33' or '-Q64'
bowtiePath string "" path with the Bowtie binaries.
kingdom string "animal" miRanalyzer parameter of either "animal" or "plant". Used to determine which set of models and features for prediction the software should use.
method string "miranalyzer" Too to use for novel miRNA discovery. One of either miranalyzer or mirdeep2.
minReadLength int 17 miRanalyzer parameter for minimum read length/bowtie seed alignment.
miranalyzer string "miRanalyzerDB/miRanalyzer.jar" Path to miranalyzer execution.
miranalyzerDB string "miRanalyzerDB/" Absolute path to miRanalyzer database.
mmToUse int 1 Number of mismatches to allow in miRanalyzer alignment (bowtie).
species string "hsa" In miranalyzer: miRBase short name of miRNA species of interest. In mirdeep2: full name of species of interest. Default is "Human".

Test cases

Test case Parameters IN
case1 (missing) fqFiles (missing) (missing) (missing) (missing) array

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