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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:

https://github.com/marvin-jens/find_circ

https://github.com/dieterich-lab/DCC

https://github.com/YangLab/CIRCexplorer