The MIRfix pipeline
MIRfix automatically curates miRNA datasets by improving alignments of their precursors, the consistency of the annotation of mature miR and miR* sequence, and the phylogenetic coverage. MIRfix produces alignments that are comparable across families and sets the stage for improved homology search as well as quantitative analyses.
The easiest way to install MIRfix or its dependencies is using bioconda. For this to work please first install conda, then configure conda to use the bioconda channel.
In short, first install conda, then run
conda config --add channels defaults
conda config --add channels bioconda
conda config --add channels conda-forge
Once conda is installed and configured, you can simply install MIRfix:
conda create -n mirfix mirfix will install MIRfix in the conda environment mirfix.
You can than use conda activate mirfix and run bash runMIRfix.sh from there.
Or you install all dependencies for MIRfix into a conda environment as follows:
In the envs directory you can find a file MIRfix.env, a simple
conda env create -f MIRfix.env will install all dependencies in the conda environment mirfix.
You can than use conda activate mirfix and run bash runMIRfix.sh from a local clone of the git repository or the unpacked source.
Make sure to fix parameters and add files according to what you want to analyze.
For a test, go to the test directory and run bash testMIRfix.sh with files and parameters for testing or the ones already provided.
Following parameters are handled by the bash wrapper around MIRfix.py:
-location: Working directory, the path to where input, output, family sequences, family names, mapping files, genomes and mature sequences are located
-cores: Number of cores for parallel processing
-extension: Number of nucleotides for extension/trimming of precursor from genomic sequence
For users who want to run the pipeline directly, following Parameters need to be set:
(cores) (outdir) (familydir) (list of families) (genomes) (mapfile) (matfile) (flank) [optional:(matrices)]
-(cores): Number of cores used for multiprocessing
-(outdir): output directory
-(familydir): Directory to fasta files of families to analyze
-(list of families): The list of families to analyze
-(genomes): The paths to the genomes where flanking regions to miRNAs can be extracted from
-(mapfile): mapping file between miRNA and miR-families
-(matfile): The mature sequences fasta file
-(flank): Number of precursor flanking nucleotides to take into account, we are using 10 in our study
-(matrices): The directory where the dialign2 matrices are located, please add the "/" at the end as in the example below Please note that when using conda there is no need for this parameter
bash runMIRfix.sh LOCATION CORES EXTENSION
To run an example, go to the directory "examples" and run the pipeline with bash testMIRfix.sh.
You can also find example files for a run there.
Please have a look at the detailed documentation in the docs folder.