Update create-a-new-project.md

AppendixAGenomeStudio/create-a-new-project.md

@@ -1,19 +1,19 @@
 # Create a New Project From .gtc and .idat Files
 
-Follow these instructions if you are starting from scratch with .idat files. Otherwise you can [open an existing project](../#/documentation/AppendixAGenomeStudio--open-an-existing-project).
+Follow these instructions if you are starting from scratch with **.idat** files. Otherwise you can [open an existing project](../#/documentation/AppendixAGenomeStudio--open-an-existing-project).
 
 1. Go to *File > New Project > Genotyping*.
 2. A pop-up window will explain which assays are supported. Click **Next**.
 3. In **Projects Repository**, choose a folder for the project.
 4. Under **Project Name**, select **Create** and name the project.
 5. Click **Next**.
 6. Select one of the following options for delineating files with sample intensities:
-    * **Use sample sheet to load sample intensities**
-    * **Load sample intensities by selecting directories with intensity files**
+    - **Use sample sheet to load sample intensities**
+    - **Load sample intensities by selecting directories with intensity files**
 7. In the next window is a text field called **SNP Manifest**. Point it to a .bpm file on your system that matches the exact version of the array that was used for genotyping. You may already have one in the same directory as the .idat files. If not, you have two options:
-    * Download one from Illumina’s website.
-    * Search the internet for the appropriate file. For example, [this is the 1000G project .bpm file](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip/broad_intensities/) (external link).
-8. In the **Data Repository** field, do not select a directory containing the .gtc and .idat files; instead select one level up. You will usually have multiple directories, each representing a sample and each containing numerous .gtc and .idat files. This list of directories will appear in Directories in Repository. Use **Add =>** to move directories that you want to analyze to Selected Directories.
+    - Download one from Illumina’s website.
+    - Search the internet for the appropriate file. For example, [this is the 1000G project .bpm file](ftp://ftp.1000genomes.ebi.ac.uk/vol1/ftp/release/20130502/supporting/hd_genotype_chip/broad_intensities/) (external link).
+8. In the **Data Repository** field, do not select a directory containing the **.gtc** and **.idat** files; instead select one level up. You will usually have multiple directories, each representing a sample and each containing numerous **.gtc** and **.idat** files. This list of directories will appear in Directories in Repository. Use **Add =>** to move directories that you want to analyze to Selected Directories.
 9. Click **Next**.
 10. In the next window, check boxes to **Cluster SNPs** and **Calculate Sample and SNP Statistics**.
 The **Gen Call Threshold** (used to determine if a genotype is called as missing or not) has a default value of 0.15, which usually is fine. Set this threshold to 0.25 if you want to keep only higher-quality genotypes.