From 7180a79938634d7e37b20304dd8ab583175d5cd8 Mon Sep 17 00:00:00 2001
From: Gregory Owens <5419829+owensgl@users.noreply.github.com>
Date: Mon, 12 Feb 2024 19:51:01 -0800
Subject: [PATCH] Update lab_6.md

---
 labs/lab_6.md | 45 +++++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 45 insertions(+)

diff --git a/labs/lab_6.md b/labs/lab_6.md
index da9c71ac3..3d8acf3dc 100644
--- a/labs/lab_6.md
+++ b/labs/lab_6.md
@@ -13,6 +13,51 @@ layout: default
 
 ****
 
+In this lab we're going to learn how to align illumina data to a reference genome. 
+This is the first step in many genomic analyses. We start off we a large number
+of anonymous reads from somewhere in the genome (or perhaps a different genome all together)
+and we need to know where they come from before we can say anything about genetic variation
+or gene expression. Log into the server to get started, and source 
+
+After logging in, lets make a new directory for this lab.
+
+```bash
+#First we source our bash profile to make sure we have access to the modules.
+source /cvmfs/soft.computecanada.ca/config/profile/bash.sh
+#Next make your new directory
+mkdir lab_6
+#And enter it
+cd lab_6
+```
+
+I've put the required files in a shared directory on the system. We'll
+copy it over to our current directory.
+```bash
+cp /project/ctb-grego/sharing/lab6_data.tar.gz ./
+```
+
+This is a tar.gz file. A tar file (originally named for tape archive) is 
+a way of putting multiple files into a single file. In our case, we are also
+gzipping it, which compresses the size. Most programs you download will be
+stored in something like a tar.gz file. Before we can access the files in the 
+tar.gz file, we have to open and unzip it. 
+```bash
+tar -xzf lab6_data.tar.gz
+```
+
+It's hard to remember the specific letter flags to use when unzipping a tar.gz file, 
+so my trick is to picture someone with a thick german accent saying "Extract Zee Files!", 
+for X, Z, F
+
+```bash
+ls
+```
+```output
+lab6_data.tar.gz  data
+```
+The data files we need 
+
+
 #Download some data
 #Download a reference genome
 #Index your reference genome