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WGBS pipeline
=============

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Preparing the VM to be able to run things
-----------------------------------------

```bash
sudo bash prepare_vm.sh
```


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Running a sample
----------------

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The reference genome is GRCh38 no alt (from ENCODE) to which I added the Lambda
phage DNA to capture methylation spike-ins. It's included in the repository.
Also included are the indices that are built using the
"bismark_genome_preparation" utility, so no need to re-run that.

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```bash
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bash wgbs-pipeline.sh /folder/with/fastqfiles/sample_id.R1.fastq.gz /folder/with/fastqfiles/sample_id.R2.fastq.gz
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```