Pipeline for iFISH single locus data analysis.
Standard iFISH single locus data analysis pipeline controlled by snakemake, a workflow management system tool to create reproducible and scalable data analyses.
IMPORTANT: before running the pipeline modify the config.yaml according to your needs, or create a new one. You can run the standard workflow using: snakemake --configfile=<your config file>
.
- Input parameters are explained in the relative section below.
- Output
- Lamina distance
- Samples
Create a subfolder in input
, where you will place a folder for each dataset. The absolute path to this folder should be specified in the config.yaml
file as deconvolved_root_folder
. The folder name must match the dataset name. Each dataset folder should contain the deconvolved tiff images, alongside a <channel>_<ID>_history.txt
file containing the deconvolution log.
Create a subfolder in input
, where you will place the automatically picked userDots tables generated with DOTTER. Each file should have the following name format: <dataset>_auto_userdots.csv
. The absolute path to this folder should be specified in the config.yaml
file as auto_userdots_folder
.