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1 |
| -# Create a New Project |
2 |
| - |
3 |
| -1. Once the directories are set up and the necessary files are in place, run **genvisis.jar**. |
4 |
| - * Linux/Mac/Running remotely on Linux |
5 |
| - * Open a terminal and run **java -Xmx#g -jar [path]/genvisis.jar** |
6 |
| - * **#g** is the number of gigabytes of memory to use |
7 |
| - * [path] is the location of the genvisis.jar file |
8 |
| - * Example |
9 |
| - * **java -Xmx24g -jar ~/genvisis.jar** (if **genvisis.jar** is saved in your home directory) |
10 |
| - * Alternatively, locate **genvisis.jar** within a file manager and double-click on the Genvisis icon |
11 |
| - * Windows |
12 |
| - * Open a text file and write inside **java -Xmx#g -jar genvisis.jar** |
13 |
| - * **#g** is the number of gigabytes of memory to use |
14 |
| - * Example |
15 |
| - * **java -Xmx24g -jar genvisis.jar** |
16 |
| - * Save the text file as **vis.bat** in the same directory as **genvisis.jar** |
17 |
| - * Double-click **vis.bat** |
| 1 | +# Create a New Project in Genvisis |
18 | 2 |
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19 | 3 | 
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20 | 4 |
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| -6. In the Genvisis window that opens, click **File** → **New Project** |
| 5 | +To create a new project, open Genvisis and then go to **File** → **New Project**. |
22 | 6 |
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23 | 7 | 
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24 | 8 |
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| -7. Enter a **Project Name** |
26 |
| -8. Click **...** next to **Project Directory** |
27 |
| -9. Choose the **[ProjectDir]** → **Select** |
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| -10. Click **...** next to **Source File Directory** |
29 |
| -11. Choose the **00src** directory created earlier → **Select** |
30 |
| -12. Genvisis will automatically detect the number of source files and the extension (eg. .csv, .csv.gz, .CEL, etc.). |
31 |
| -13. Choose the **Array Type** with which the data was collected: |
| 9 | +1. Enter a **Project Name** |
| 10 | +2. Click **...** next to **Project Directory** |
| 11 | +3. Choose the **[ProjectDir]** → **Select** |
| 12 | +4. Click **...** next to **Source File Directory** |
| 13 | +5. Choose the **00src** directory created earlier → **Select** |
| 14 | +6. Genvisis will automatically detect the number of source files and the extension (eg. .csv, .csv.gz, .CEL, etc.). |
| 15 | +7. Choose the **Array Type** with which the data was collected: |
32 | 16 | * ILLUMINA
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33 | 17 | * AFFY_GW6
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34 | 18 | * Only SNP probesets
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41 | 25 | * CEL files
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42 | 26 | * APT results
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43 | 27 | * Must have the same name as the **Project Name**
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44 |
| -14. **Genome Build** allows you to specify which version of the human genome to run the project in (e.g., **[Genome Reference Consortium Human Build 38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/)** (external link) aka **GRCh38**). |
| 28 | +8. **Genome Build** allows you to specify which version of the human genome to run the project in (e.g., **[Genome Reference Consortium Human Build 38](https://www.ncbi.nlm.nih.gov/assembly/GCF_000001405.26/)** (external link) aka **GRCh38**). |
45 | 29 | * Unless there is a specific need to use an older version of the genome, set **Genome Build** to **HG38**, even if the manifest is in an older build. Genvisis can remap marker positions to **hg38** in the [Create Marker Positions](../#/documentation/RunTheGenvisisWorkflow--create-marker-positions-illumina) step of the Workflow.
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46 | 30 | * To determine which version of the genome your data is in, check the **GenomeBuild** column of your Illumina manifest, or the header of your Affymetrix manifest.
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47 |
| -15. Select the locations for the following files: |
| 31 | +9. Select the locations for the following files: |
48 | 32 | * **Illumina Manifest File** (if applicable)
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49 | 33 | * **Pedigree File**
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50 | 34 | * **Sample ID Linker File**
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51 | 35 | * **Batch File**
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52 | 36 | * **Marker Subset File**
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53 | 37 | * Used only if you are not analyzing all markers in the manifest
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54 |
| -16. If using Illumina reports, **Create** will launch the **Validation Review** window. Fields will be automatically populated from the source files. |
| 38 | +10. If using Illumina reports, **Create** will launch the **Validation Review** window. Fields will be automatically populated from the source files. |
55 | 39 | * Required
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56 | 40 | * **Marker Name**
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57 | 41 | * **Sample ID**
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68 | 52 |
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69 | 53 | 
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70 | 54 |
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| -17. If the reports don’t have consistent headers, there will be a separate validation review window for each group of reports. |
72 |
| -18. Click **OK**. |
73 |
| -19. An audit will be performed to verify that the markers in the manifest are either 100% congruent with one of the reports, or that both the manifest and a report are 100% congruent with the Marker Subset File if one is provided. |
| 55 | +11. If the reports don’t have consistent headers, there will be a separate validation review window for each group of reports. |
| 56 | +12. Click **OK**. |
| 57 | +13. An audit will be performed to verify that the markers in the manifest are either 100% congruent with one of the reports, or that both the manifest and a report are 100% congruent with the Marker Subset File if one is provided. |
74 | 58 | * If the manifest and the examined report match, a new project will be created and a new window will appear: **[Genvisis Project Workflow](../#/documentation/RunTheGenvisisWorkflow--introduction-to-the-workflow)**
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75 | 59 | * If the manifest and examined report do not match, project creation will fail and you will need to create a Marker Subset File that lists only the markers shared between both files.
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76 |
| -20. If using Affymetrix CEL files, there will be no Validation Review and Genvisis will go directly to the **[Project Workflow](../#/documentation/RunTheGenvisisWorkflow--introduction-to-the-workflow)**. |
77 |
| -21. Several new files will be generated. Inside **[ProjectDir]** will be a file named **source_headers.ser** and the new sub-directory **logs/**. Inside **data/** will be the file **import.ser**. |
| 60 | +14. If using Affymetrix CEL files, there will be no Validation Review and Genvisis will go directly to the **[Project Workflow](../#/documentation/RunTheGenvisisWorkflow--introduction-to-the-workflow)**. |
| 61 | +15. Several new files will be generated. Inside **[ProjectDir]** will be a file named **source_headers.ser** and the new sub-directory **logs/**. Inside **data/** will be the file **import.ser**. |
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