iguigon/mirkwood repository overview

miRkwood is a software package for the discovery of microRNAs and their hairpin precursors in plant genomes. It combines multiple evidences to support the prediction: thermodynamical stability, conservation, miRNA:miRNA* duplex,...

miRkwood website: https://bioinfo.cristal.univ-lille.fr/mirkwood/mirkwood.php⁠

It comes in two versions.

• mirkwood ab initio, for the analysis of raw genomic sequences
• mirkwood small RNA-seq, for the analysis of deep sequencing data

Usage:

1. Abinitio pipeline:

Here is an example of command line for abinitio pipeline:

sudo docker run -v /your/mapping/repertory/:/MAPPING/
iguigon/mirkwood
mirkwood.pl
--input /MAPPING/input/sequenceSomething.fas
--output /MAPPING/output/results_abinitio
--filter-rrna --filter-trna --varna

Type the following command for detailed help on the command options: sudo docker run iguigon/mirkwood mirkwood.pl --help

1. SmallRNAseq pipeline:

miRkwood smallRNAseq pipeline takes as input a BED file with the following syntax:

1 18092 18112 AAACGTGTAGAGAGAGACTCA 1 -

1 18094 18118 GATTCTTTTGTTTGCCACT 2 +

1 18096 18119 TCGATAGGATCAAGTACATCT 1 +

1 18100 18124 AAGAAGAAAAAGAAGAAGAAGAAG 9 +

In this file, each line is a unique read. The fields are, from left to right: name of the chromosome, starting position, ending position, read sequence, number of occurrences of the read in the data, strand. Positions follow the BED numbering convention: the first base of the chromosome is considered position 0 (0-based position) and the feature does not include the stop position.

You can convert a BAM file into the needed BED format with our custom script: sudo docker run -v /your/mapping/repertory/:/MAPPING/
iguigon/mirkwood
mirkwood-bam2bed.pl
--in /MAPPING/input.bam
--bed /MAPPING/output.bed
--min 18
--max 25

Type the following command for detailed help on the command options: sudo docker run iguigon/mirkwood mirkwood-bam2bed.pl --help

Here is an example of command line for smallRNAseq pipeline:

sudo docker run -v /your/mapping/repertory/:/MAPPING/
iguigon/mirkwood
mirkwood-bed.pl
--input /MAPPING/input/sample.bed
--output /MAPPING/output/results_smallRNAseq
--genome /MAPPING/input/my_genome.fasta
--mirbase /MAPPING/input/my_mirbase_file.gff3
--gff /MAPPING/input/my_annotations_file.gff
--min-repeats 0
--max-repeats 5
--align

Type the following command for detailed help on the command options: sudo docker run iguigon/mirkwood mirkwood-bed.pl --help

With the -v /your/mapping/repertory/:/MAPPING/ parameter, Docker will mount your local folder /your/mapping/repertory/ into the container under /home/mapping/. Make sure you have stored all your needed input files in this folder. Results files will be stored here as well.

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