For complete documentation for circs_snake please open circs_snake_manual.md in this repo

circs_snake: a snakemake workflow for circular RNA detection and quantification based on find_circ, DCC and CIRCexplorer1.

how to get started

get the code: git clone https://github.com/daaaaande/circs_snake
personalize: nano config.yaml
prepare: copy/move your input files (paired RNAseq .fastq files) to circs_snake/.
also create samplesheet needed: more in the config/ readme
run: snakemake -n (remove the -n once everything looks OK)

additional credits to the original pipelines authors:

Name		Name	Last commit message	Last commit date
Latest commit History 31 Commits
config		config
cx		cx
data		data
dcc		dcc
envs		envs
f_c		f_c
scripts		scripts
.gitignore		.gitignore
.snakemake-workflow-catalog.yml		.snakemake-workflow-catalog.yml
LICENSE		LICENSE
README.md		README.md
Snakefile		Snakefile
circs_snake_manual.md		circs_snake_manual.md
cluster.json		cluster.json
config.yaml		config.yaml
config_hg38.yaml		config_hg38.yaml
example_dag_5_samples.svg		example_dag_5_samples.svg
get_new_genomes.sh		get_new_genomes.sh
how_to_run_circrna_pipeline.txt		how_to_run_circrna_pipeline.txt
howtostart.sh		howtostart.sh
pipeline_execution.sh		pipeline_execution.sh
samples.tsv		samples.tsv