iFISH-singleLocus-analysis

Pipeline for iFISH single locus data analysis.

Motivation

Standard iFISH single locus data analysis pipeline controlled by snakemake, a workflow management system tool to create reproducible and scalable data analyses.

Requirements

• pygpseq
• snakemake

Setup and run

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>.

Config file parameters

• Input parameters are explained in the relative section below.
• Output
• Lamina distance
• Samples

Input

Deconvolved images, by Huygens (or similar)

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.

Automatically picked userDots

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.

Workflow