Up: Component summary
Up: Component summary
Function
NovelMirnas
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 |
Inputs| 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). |
Outputs| Name | Type | Description |
|---|---|---|
| array | Array<BinaryFile> | Array of miRDeep2 results. |
Parameters| 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 fqFiles |
IN mirDP_genome |
IN mirDP_mature |
IN mirDP_related_mature |
IN mirDP_precursor |
OUT array |
|---|---|---|---|---|---|---|---|
| case1 | (missing) | fqFiles | (missing) | (missing) | (missing) | (missing) | array |