Update manipulating_vcf.md

docs/Case_studies/manipulating_vcf.md

@@ -33,22 +33,31 @@ Finally, full gene names and functions found in this [file](https://ftp.flybase.
 
 * For shorter run times, extract chromosome 4 and look only at that.
 
-#### Chromosome 4
+### Making awking the data easier
+Start by splitting the task into sub-tasks. This makes it easier to see what happens and you might get interesting intermediary results. 
 
-??? "_Hint_ **What do we need?**"
-    Extract chr4 from the vcf and the gff and make new files
+### *bonus result* 
+A table with counted and sorted different genomic features in chromosome 4.
 
-??? "_Hint_"
-    All lines from chromosome 4 start with a *4*
+### *bonus result* 
+SNPs sorted by number. Just like the coins on day one.
 
-??? "_Solution_"
-    `awk '/^4/{print $0}' Drosophila_melanogaster.BDGP6.28.101.gff3 > Drosophila_melanogaster.chr4.gff3`
-
-    `awk '/^4/{print $0}' dgrp2_trimmed.vcf > dgrp2_chr4.vcf`
+### The exercise
+Identify the steps you need and use awk to do those. Open the hints if you get stuck.
+
+
+<br>
+<br>
+<br>
+<br>
+<br>
+<br>
 
 
-#### Making awking the data easier
-Start by splitting the task into sub-tasks. This makes it easier to see what happens and you might get interesting intermediary results. 
+
+## Hints, ordered by subject. Don't use them unless necessary.
+
+### Overall, an example of things to look for
 
 ??? "_Hint_ **Example**"
     Let's say we want to find out all genes that contains a variant and all variants that are located within a gene. What do we want to do first? Take a look at the vcf file. That is the one that contains all the variants. Then look at the gff file, which contains the genes and other annotations. Finally, take a look at the DNA sequence. You will need to combine all three to answer the question. 
@@ -59,25 +68,19 @@ Start by splitting the task into sub-tasks. This makes it easier to see what hap
     * Separation of variants (SNPs and INDELs) into two groups, inside and outside genes (and CDSs)
     * Separation of genes/CDSs into those with and without variants (and maybe how many there are per gene)
 
-### The exercise
-Identify the steps you need to do and what each step does. Open the hints if you get stuck.
-
-#### *bonus result* 
-A table with counted and sorted different genomic features in chromosome 4.
+### Chromosome 4
 
-#### *bonus result* 
-SNPs sorted by number. Just like the coins on day one.
-
-<br>
-<br>
-<br>
-<br>
-<br>
-<br>
+??? "_Hint_ **What do we need?**"
+    Extract chr4 from the vcf and the gff and make new files
 
+??? "_Hint_"
+    All lines from chromosome 4 start with a *4*
 
+??? "_Solution_"
+    `awk '/^4/{print $0}' Drosophila_melanogaster.BDGP6.28.101.gff3 > Drosophila_melanogaster.chr4.gff3`
+
+    `awk '/^4/{print $0}' dgrp2_trimmed.vcf > dgrp2_chr4.vcf`
 
-## Hints, don't use unless necessary.
 
 
 ??? "_bonus result example_ **A table with counted and sorted different genomic features in chromosome 4.**"