domonik / syndeseq

Synechocystis RNAlocSeq Analysis

This repository contains a pipeline to analyze RNAloc-Seq Data from Synechocystis. The Pipeline can be run automatically via installing the conda environment from env.yml

conda env create -f env.yml

If you have the Data folder you can run the pipeline via

Warning The Data is not publically available yet

snakemake -s deseqpipeline.smk --cores 1 -k

This produces the PipelineData directory where you can find all important files.

The files within this directory contain wildcards, which map the to the corresponding analysis pipeline. The following Table describes the abbreviations used in file names:

Abbreviation	Values	Description
set	Light, LightDark, LightDarkLight	The Dataset used. Light contains everything but the Puromycin columns from the Light Dataset. LightDark represents the Light part of the LightDark Dataset LightDarkLight is the merged Dataset containing all Light columns from the Light and LightDark Dataset
design	rf	A mapping mapping the abbreviation to the design formula used in DESeq2. rf: "~ replicate + fraction"
cond	M, TC, C	Which fraction to compare: M: Membrane C: Cytosol TC: Total Cell
base	M, TC, C	The base to compare cond to. See cond for description
ud	upregulated, downregulated	Only present in Enrichment files. Shows whether the file shows up or downregulated enriched set.
ont	MF, BP, CC	Ontology subcategory: Molecular Function, Biological Process, Cellular Compartment