Experiment Protocol by Markdown Example
=======================================

For today's experiment we will be analyzing the following
blockquote:

> ...the **twist** transcription factor binds broadly
> across the genome and regulates important developmental
> events.

### What we need

To accomplish this we need three things from the following list:

* an installed aligner
* a working directory
* a set of [fastq files](http://compgenomics/Data/ChIP-Seq/)

The mutants are summarized in the following Table:

Mutation | Dorsal | Result
-------- | ------ | ------
gd7      | none   | gd7_1.fastq.gz
Tol10b   | high   | tol10b_1.fastq.gz

The steps we will take are indicated in this ordrered list:

1. Create a working directory
2. write a simple alignment script
    * see the class examples
3. check the server *before* we run the script

#### We also need to write some shell code 

our script might look something like:

```shell
    for f in FILES
    do
      tophat f
    done
```

We ran it on maple, which has ~~12 cores~~ 24 cores.

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