motif_check

Evaluate de novo motif finding tools. Create precision/recall plots and compute performance metrics, by labeling motifs around ChIP-seq summits as positives.

download

Execute the following command.

git clone https://github.com/aryarm/motif_check.git

setup

The pipeline is written as a Snakefile which can be executed via Snakemake. We recommend installing version 6.4.1:

conda create -n snakemake -c bioconda -c conda-forge --no-channel-priority 'snakemake==6.4.1'

We highly recommend you install Snakemake via conda like this so that you can use the --use-conda flag when calling snakemake to let it automatically handle all dependencies of the pipeline. Otherwise, you must manually install the dependencies listed in the env files.

execution

Activate snakemake via conda:
```
conda activate snakemake
```
Execute the pipeline on the example data

Locally:
```
./run.bash &
```

Output

VarCA will place all of its output in a new directory (out/, by default). Log files describing the progress of the pipeline will also be created there: the log file contains a basic description of the progress of each step, while the qlog file is more detailed and will contain any errors or warnings.

Executing the pipeline on your own data

You must modify the config.yaml file to specify paths to your data. The config file is currently configured to run the pipeline on the example data provided.

If this is your first time using Snakemake

We recommend that you run snakemake --help to learn about Snakemake's options. For example, to check that the pipeline will be executed correctly before you run it, you can call Snakemake with the -n -p -r flags. This is also a good way to familiarize yourself with the steps of the pipeline and their inputs and outputs (the latter of which are inputs to the first rule in each workflow -- ie the all rule).

Note that Snakemake will not recreate output that it has already generated, unless you request it. If a job fails or is interrupted, subsequent executions of Snakemake will just pick up where it left off. This can also apply to files that you create and provide in place of the files it would have generated.

By default, the pipeline will automatically delete some files it deems unnecessary (ex: unsorted copies of a BAM). You can opt to keep these files instead by providing the --notemp flag to Snakemake when executing the pipeline.