This is a snakemake pipeline to detect miRNA in samples.
You will need to edit your config file as described below:
Config Variable | Description |
---|---|
SAMPLES | name of file containing your samples names, default: samples.tsv |
GENOME | Path to your genome file |
PREFIX | Name of the prefix of the genome to align to "mature" |
miRNA | default is "mature.fa" pulled automatically from mirbase |
PAIRED | True if your samples are paired, false otherwise |
The pipeline takes samples with a suffix 'r_1.fq.gz' and 'r_2.fq.gz' if the samples are paired. Or it takes samples with suffix 'fq.gz' if the samples is single-end reads.
Regardless your samples are paired, single-ended, samples names should be samples.tsv without the suffix.
The pipeline uses by default "mature.fa" from mirbase.
snakemake -jn
where n is the number of cores for example for 10 cores use:
snakemake -j10
For less froodiness, use conda:
snakemake -jn --use-conda
For example, for 10 cores use:
snakemake -j10 --use-conda
This will pull automatically the same versiosn of tools we used. Conda has to be installed in the system, in addition to snakemake.
For a dry run use:
snakemake -j1 -n
and to print command in dry run use:
snakemake -j1 -n -p
Just update your config file to include all your sample names, edit your interval.list file to include your intervals of interest, your path, etc for example:
snakemake -j1 --configfile config-WES.yaml
or:
snakemake -j1 configfile config-WGS.yaml