Module: rje_miRNA Description: Miscellaneous miRNA Analysis Module Version: 0.3 Last Edit: 15/07/13

Copyright © 2008 Richard J. Edwards - See source code for GNU License Notice

Imported modules: rje rje_db rje_seq rje_slim rje_zen slimfinder

See SLiMSuite Blog for further documentation. See rje for general commands.

Function

This module controls various custom miRNA analyses. It is envisioned that it will be replaced in time with other modules.

Commandline

INPUT

seqin=FILE : Main file for analysis, containing UTRs []
maxseq=X : Maximum number of sequences to process [500]
seedfreq=T/F: Whether to use overall Seed Frequencies per sequence for slimprob [False]

ANALYSIS

run=LIST : List of analyses/manipulations (nrutr/enspita/cleal) []
enspath=PATH: Path to EnsLoci files [/scratch/Databases/NewDB/EnsEMBL/]

CLEAL Analysis

minmax=X : Minimum value for Maximum expression value [1.0]
arraydata=FILE : File of array data for Cleal analysis []
miranda=FILE : Miranda prediction file []
validated=FILE : Validate mRNA target file []

History Module Version History

    # 0.0 - Initial Compilation.
    # 0.1 - Shifted focus of analysis to use PITA instead.
    # 0.2 - Added Cleal Analysis of Placental versus miRanda downloads (http://www.microrna.org/microrna/getDownloads.do)
    # 0.3 - Tidied up some import calls.