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NovelMatureSeq

Given a set of putative novel miRNA regions (e.g. output from miRanalyzer or miRDeep2), retrieves consensus functional "mature" region that can then be used for predicting target genes (e.g. as input to MirMatch.

Version 0.1
Bundle sequencing
Categories Novel smallRNA
Authors Katherine Icay (katherine.icay@helsinki.fi)
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Source files component.xml novelMatureSeq.r
Usage Example with default values

Inputs

Name Type Mandatory Description
novel CSV Mandatory Input CSV file with first column containing putative novel miRNA coordinates (chr, start, end, and strand separated by "_"). Recommended input is a subset of interesting putative novel miRNAs, or the output of DEan.
fqFiles CSV Mandatory This should be the same input file used in miRanalyzer. List of reads mapped to the genome but not mapped to any known miRNAs, with unique sample ID in the first column.

Outputs

Name Type Description
mature CSV The input CSV file 'novel' with an additional "predicted_mature" column containing the consensus mature sequence across samples.
array Array<CSV> Array with a file for each entry in the 'novel' input, containing the putative functional mature sequence for all samples analyzed.

Parameters

Name Type Default Description
execDir string "" Required! Path to execution directory containing the miRanalyzer results for each sample in the fqFiles list.
execPrefix string "mirA" Prefix attached to the instance produced by novelMirnas function.

Test cases

Test case Parameters IN
novel
IN
fqFiles
OUT
mature
OUT
array
case1 properties novel fqFiles mature (missing)

execDir=relations,
execPrefix=mirA


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