GRAVI: Gene Regulatory Analysis using Variable Inputs
This is a snakemake
workflow for:
- Performing sample QC
- Calling ChIP peaks
- Performing Differential Binding Analysis
- Comparing results across ChIP targets
The minimum required input is one ChIP target with two conditions.
Full documentation can be found here
Snakemake Implementation
The basic workflow is written snakemake
, requiring at least v7.7, and can be called using the following steps.
Firstly, setup the required conda environments
snakemake \
--use-conda \
--conda-prefix '/home/steveped/mambaforge/envs/' \
--conda-create-envs-only \
--cores 1
Secondly, create and inspect the rulegraph
snakemake --rulegraph > workflow/rules/rulegraph.dot
dot -Tpdf workflow/rules/rulegraph.dot > workflow/rules/rulegraph.pdf
Finally, the workflow itself can be run using:
snakemake \
-p \
--use-conda \
--conda-prefix '/home/steveped/mambaforge/envs/' \
--notemp \
--rerun-triggers mtime \
--keep-going \
--cores 16
Note that this creates common environments able to be called by other workflows and is dependent on the user.
For me, my global conda environments are stored in /home/steveped/mambaforge/envs/
.
For other users, this path will need to be modified.
If wishing to tidy the directory after a successful run, you can check which non-essential files can be deleted using snakemake -n --delete-temp-output --cores 1
.
If the files earmarked for deletion are considered to be non-essential, they can be deleted by removing the -n
flag from the above code: snakemake --delete-temp-output --cores 1
.
As the bedgraph files produced by macs2 callpeak
are typically very large, hence their conversion to bigwig files during the workflow, this step can free a considerable amount of disk space.
Version History
v0.1.5d (earliest) Created 21st Mar 2023 at 05:48 by Stevie Pederson
Final bugfix in replicate venn-plot
Frozen
v0.1.5d
b876eae
Creator
Submitter
Views: 152 Downloads: 41
Created: 21st Mar 2023 at 05:48
None