Update lab_7.md

labs/lab_7.md

@@ -13,4 +13,64 @@ layout: default
 
 ****
 
-When we 
+When we are resequencing a species with a reference genome, the ultimate goal is to 
+detect where your new sample differs from the reference genome and how multiple
+samples differ from each other. To do this, we are going to use the aligned sequence
+data to call variants. 
+
+First thing, log into the server and remember to source your bash.sh file so that you have access to the modules.
+
+I've supplied you with aligned bam files and a reference genomes on the server at "/project/ctb-grego/sharing/lab_7". 
+
+```bash
+ls -R /project/ctb-grego/sharing/lab_7
+```
+```output
+bam  reference
+
+/project/ctb-grego/sharing/lab_7/bam:
+sample_0.bam      sample_2.bam.bai  sample_5.bam      sample_7.bam.bai
+sample_0.bam.bai  sample_3.bam      sample_5.bam.bai  sample_8.bam
+sample_1.bam      sample_3.bam.bai  sample_6.bam      sample_8.bam.bai
+sample_1.bam.bai  sample_4.bam      sample_6.bam.bai  sample_9.bam
+sample_2.bam      sample_4.bam.bai  sample_7.bam      sample_9.bam.bai
+
+/project/ctb-grego/sharing/lab_7/reference:
+SalmonReference.fasta
+```
+We could copy those files into your home directory, but that would mean there will be a different
+copy for every student. When files are very large or there are many users that can be a problem. 
+Instead, we're going to create a symbolic link. This looks like a file on your system, and you can use it like a file,
+but the orginal data stays in one spot and isn't copied. 
+
+```bash
+#Make a directory for the new bam file links to go
+mkdir lab_7/bam
+cd lab_7/bam
+
+#Link all the bam files
+ln -s /project/ctb-grego/sharing/lab_7/bam/* ./
+
+#Take a look and see if it worked.
+ls
+```
+
+```output
+sample_0.bam      sample_2.bam.bai  sample_5.bam      sample_7.bam.bai
+sample_0.bam.bai  sample_3.bam      sample_5.bam.bai  sample_8.bam
+sample_1.bam      sample_3.bam.bai  sample_6.bam      sample_8.bam.bai
+sample_1.bam.bai  sample_4.bam      sample_6.bam.bai  sample_9.bam
+sample_2.bam      sample_4.bam.bai  sample_7.bam      sample_9.bam.bai
+```
+
+Now lets do the same for the reference genome
+```bash
+mkdir ../reference
+cd ../reference
+ln -s /project/ctb-grego/sharing/lab_7/reference/* ./
+```
+
+
+
+
+