TimEX Tutorial - Revision history

Julien: /* Computing the Correlation Coefficient */

2014-04-21T21:11:36Z

‎Computing the Correlation Coefficient

Julien: /* Saturating and Indexing the layers */

2014-04-21T21:11:21Z

‎Saturating and Indexing the layers

Julien: /* Gaussing the layers */

2014-04-21T21:10:53Z

‎Gaussing the layers

Julien: /* Computing the ratio S / G1 */

2014-04-21T21:10:26Z

‎Computing the ratio S / G1

Julien: /* Normalizing the layers */

2014-04-21T21:09:59Z

‎Normalizing the layers

Julien: /* Filtering the G1 layers */

2014-04-21T21:09:44Z

‎Filtering the G1 layers

Julien: /* Load the Files */

2014-04-21T21:09:12Z

‎Load the Files

Julien: /* Computing the Correlation Coefficient */

2014-04-21T21:08:21Z

‎Computing the Correlation Coefficient

Julien: /* Saturating and Indexing the layers */

2014-04-21T21:07:59Z

‎Saturating and Indexing the layers

Julien: /* Gaussing the layers */

2014-04-21T21:07:14Z

‎Gaussing the layers

@@ Line 86: / Line 86: @@
 == Computing the Correlation Coefficient ==
-The last step is to compute the correlation coefficient between these two layers. To do so you need to select the Layer > Correlation option of the contextual menu.  When asked choose the second layer for the correlation.  A window showing the correlation coefficient for each chromosome as well as the genome wide correlation should pop-up (figure 18).
+The last step is to compute the correlation coefficient between these two layers. To do so you need to select the Layer > Correlation option of the contextual menu.  When asked choose the second layer for the correlation.  A window showing the correlation coefficient for each chromosome as well as the genome wide correlation should pop-up (figure 20).
-[[image:TimEX_Tutorial_Correlation_Coefficients.png|center|frame|Figure 18: Correlation Coefficients]]
+[[image:TimEX_Tutorial_Correlation_Coefficients.png|center|frame|Figure 20: Correlation Coefficients]]

@@ Line 75: / Line 75: @@
 To make the tracks easier to compare we need to index (rescale) them between 0 and 100.
-Before indexing the data we want to saturate the 1% greatest and smallest value in order to reduce the effect of eventual outliers.  To saturate the track you need to right click on the track handler and select the Layer > Filter menu (Figure 14).  On the filter option select the percentage filter and set the parameters as shown on figure 15. You need to do this operation for the ES and ERY tracks.
+Before indexing the data we want to saturate the 1% greatest and smallest value in order to reduce the effect of eventual outliers.  To saturate the track you need to right click on the track handler and select the Layer > Filter menu (Figure 16).  On the filter option select the percentage filter and set the parameters as shown on figure 17. You need to do this operation for the ES and ERY tracks.
-Now we need to index the two tracks.  Select one of the track, right click on the track handler to show the contextual menu and click on the Layer > Index option (Figure 16).  Set the new minimum to 0 and the new maximum to 100. Select ''No'' when asked to index the chromosomes independently. Repeat the operation for the second track.  The result should be similar to what is shown on figure 17.
+Now we need to index the two tracks.  Select one of the track, right click on the track handler to show the contextual menu and click on the Layer > Index option (Figure 18).  Set the new minimum to 0 and the new maximum to 100. Select ''No'' when asked to index the chromosomes independently. Repeat the operation for the second track.  The result should be similar to what is shown on figure 19.
-[[image:TimEX_Tutorial_Saturate_Menu.png|center|frame|Figure 14: Saturate Menu]]
+[[image:TimEX_Tutorial_Saturate_Menu.png|center|frame|Figure 16: Saturate Menu]]
-[[image:TimEX_Tutorial_Saturate_Options.png|center|frame|Figure 15: Saturate Options]]
+[[image:TimEX_Tutorial_Saturate_Options.png|center|frame|Figure 17: Saturate Options]]
-[[image:TimEX_Tutorial_Index_Menu.png|center|thumb|800px|Figure 16: Index Menu]]
+[[image:TimEX_Tutorial_Index_Menu.png|center|thumb|800px|Figure 18: Index Menu]]
-[[image:TimEX_Tutorial_Index_Result.png|center|frame|Figure 17: Index Result]]
+[[image:TimEX_Tutorial_Index_Result.png|center|frame|Figure 19: Index Result]]
 == Computing the Correlation Coefficient ==

@@ Line 65: / Line 65: @@
 So far, three smoothing algorithms had been incorporated to GenPlay: the moving average smoothing, the Gaussian smoothing and the Loess smoothing.  In practice these three operations produce pretty similar results.
-To gauss the layers, first right click on one of the two S / G1 track handler and select the Smoothing option of the layer menu (Figure 11). Then, select the Gaussian algorithm. We need to set the gaussian smoothing parameter Sigma. We set Sigma to 100kb for this experiment (which correspond to a moving window of 400kb, Figure 12). Don't extrapolate the result to null windows when prompted.
+To gauss the layers, first right click on one of the two S / G1 track handler and select the Smoothing option of the layer menu (Figure 13). Then, select the Gaussian algorithm. We need to set the gaussian smoothing parameter Sigma. We set Sigma to 100kb for this experiment (which correspond to a moving window of 400kb, Figure 14). Don't extrapolate the result to null windows when prompted.
-Repeat the operation for the second layer.  The figure 13 show the result of the smoothing.
+Repeat the operation for the second layer.  The figure 15 show the result of the smoothing.
-[[image:TimEX_Tutorial_Gaussian_Menu.png|center|frame|Figure 11: Smoothing Menu]]
+[[image:TimEX_Tutorial_Gaussian_Menu.png|center|frame|Figure 13: Smoothing Menu]]
-[[image:TimEX_Tutorial_Sigma_Selection.png|center|frame|Figure 12: Sigma Selection]]
+[[image:TimEX_Tutorial_Sigma_Selection.png|center|frame|Figure 14: Sigma Selection]]
-[[image:TimEX_Tutorial_Gaussian_Result.png|center|frame|Figure 13: Gaussian Smoothing Result]]
+[[image:TimEX_Tutorial_Gaussian_Result.png|center|frame|Figure 15: Gaussian Smoothing Result]]
 == Saturating and Indexing the layers ==

@@ Line 51: / Line 51: @@
 == Computing the ratio S / G1 ==
-The next step is to generate new layers representing the ratio S / G1 for each cell type.  To do that you need to right click on the hES-S track handler and then to select the "Two Tracks Operation" option of the Layer menu (Figure 8).  After that, you need to select the hES-G1 layer when prompted (Figure 9).  Select a track where you want to generate the result and select the division operation.
+The next step is to generate new layers representing the ratio S / G1 for each cell type.  To do that you need to right click on the hES-S track handler and then to select the "Two Tracks Operation" option of the Layer menu (Figure 10).  After that, you need to select the hES-G1 layer when prompted (Figure 11).  Select a track where you want to generate the result and select the division operation.
-After repeating the same operation with the erythroid tracks the result should be similar to the one on figure 10.
+After repeating the same operation with the erythroid tracks the result should be similar to the one on figure 12.
-[[image:TimEX_Tutorial_2_Layers_operation_Menu.png|center|frame|Figure 8: Two Layers Operation Menu]]
+[[image:TimEX_Tutorial_2_Layers_operation_Menu.png|center|frame|Figure 10: Two Layers Operation Menu]]
-[[image:TimEX_Tutorial_2nd_Layer_Dialog.png|center|frame|Figure 9: Second Layer Dialog]]
+[[image:TimEX_Tutorial_2nd_Layer_Dialog.png|center|frame|Figure 11: Second Layer Dialog]]
-[[image:TimEX_Tutorial_S_On_G1_Result.png|center|frame|Figure 10: S / G1 Result]]
+[[image:TimEX_Tutorial_S_On_G1_Result.png|center|frame|Figure 12: S / G1 Result]]
 == Gaussing the layers ==

@@ Line 43: / Line 43: @@
 The normalize operation of GenPlay divides each score by the some of all the scores of the layer and multiply the result by a large constant specified by the user.  The only purpose of the constant is to make the score more readable.
-Let's start by normalizing the hES-G1 layer. You need first to right click on the track handler.  After that, select the normalize option of the layer sub-menu as shown on figure 7. You can keep the default constant, just click OK. After that operation the score are expressed as number of read per window per 100 billion reads (if you kept the default constant) because the window score represents the sum of the reads that mapped to that window, the total of all the score is therefore the total number of reads.
+Let's start by normalizing the hES-G1 layer. You need first to right click on the track handler.  After that, select the normalize option of the layer sub-menu as shown on figure 9. You can keep the default constant, just click OK. After that operation the score are expressed as number of read per window per 100 billion reads (if you kept the default constant) because the window score represents the sum of the reads that mapped to that window, the total of all the score is therefore the total number of reads.
 After normalization each score is equal to (# of read per window *100,000,000,000) / total # of reads.
 Once normalization is done for the first layer. The three other layers are processed in the same manner.
-[[image:TimEX_Tutorial_Normalize.png|center|thumb|800px|Figure 7: Normalize]]
+[[image:TimEX_Tutorial_Normalize.png|center|thumb|800px|Figure 9: Normalize]]
 == Computing the ratio S / G1 ==

@@ Line 31: / Line 31: @@
 This step is necessary becasue we found that windows with low number of reads were increasing the signal to noise ratio because of excessive sampling errors.
-To filter the windows with less than 8 reads, right-click on the hES-G1 track handler, select the layer operation menu at the bottom of the contextual menu and then select the filter sub-menu (figure 4).
+To filter the windows with less than 8 reads, right-click on the hES-G1 track handler, select the layer operation menu at the bottom of the contextual menu and then select the filter sub-menu (figure 6).
-Then select the Threshold filter option and set the values as shown on figure 5. Click on OK in order to remove all the windows with a score smaller than 8. The result is shown on figure 6.
+Then select the Threshold filter option and set the values as shown on figure 7. Click on OK in order to remove all the windows with a score smaller than 8. The result is shown on figure 8.
-[[image:TimEX_Tutorial_Filter_Menu.png|center|thumb|800px|Figure 4: Filter Menu]]
+[[image:TimEX_Tutorial_Filter_Menu.png|center|thumb|800px|Figure 6: Filter Menu]]
-[[image:TimEX_Tutorial_Filter Dialog.png|center|frame|Figure 5: Threshold Filter]]
+[[image:TimEX_Tutorial_Filter Dialog.png|center|frame|Figure 7: Threshold Filter]]
-[[image:TimEX_Tutorial_Filter_Result.png|center|thumb|800px|Figure 6: Filter Result]]
+[[image:TimEX_Tutorial_Filter_Result.png|center|thumb|800px|Figure 8: Filter Result]]
 == Normalizing the layers ==

@@ Line 17: / Line 17: @@
 The first thing to do is to download the four files used during this tutorial.  The files are available [http://www.genplay.net/library/tutorials/TimEX/ here] (if your web-browser opens the files in a new tab or window, please select the Save As option of the File menu of your browser to retrieve the files).
-Once GenPlay is started, right click on the track handler of the 1st row, in order to open a contextual menu that will allow you to load layers (figure 1). Select ''Add Layer(s)'' (figure 2), then select the hES-G1.bed file and choose ''Variable or Fixed Window Layer''.
+Once GenPlay is started, right click on the track handler of the 1st row, in order to open a contextual menu that will allow you to load layers (figure 3). Select ''Add Layer(s)'' (figure 4), then select the hES-G1.bed file and choose ''Variable or Fixed Window Layer''.
-[[image:TimEX_Tutorial_Add_layer.png|center|thumb|800px|Figure 1: Add Layer(s) Menu]]
+[[image:TimEX_Tutorial_Add_layer.png|center|thumb|800px|Figure 3: Add Layer(s) Menu]]
-[[image:TimEX_Tutorial_Layer_Type.png|center|frame|Figure 2: Layer Type]]
+[[image:TimEX_Tutorial_Layer_Type.png|center|frame|Figure 4: Layer Type]]
-After selecting the ES G1 file and the layer type, an option window is going to prompt you to enter information on how to load the data. You can keep the default name for the layer or change it if you prefer. Then, you need to check the ''Bin Data'' option and to choose a window size and a method of score calculation. The size of the windows that you should choose depends on the number of reads that are available. For timing of replication studies, we can choose a window size of 5,000bp.  The option for the score calculation are discussed in the Documentation.  For the type of files used in this example, you should choose sum as the method for the score calculation.  You can keep the default data precision.
+After selecting the ES G1 file and the layer type, an option window is going to prompt you to enter information on how to load the data. You can keep the default name for the layer or change it if you prefer. Then, you need to check the ''Bin Data'' option and to choose a window size and a method of score calculation. The size of the windows that you should choose depends on the number of reads that are available. For timing of replication studies, we can choose a window size of 5,000bp.  The option for the score calculation are discussed in the Documentation.  For the type of files used in this example, you should choose sum as the method for the score calculation.
-[[image:TimEX_Tutorial_New_Layer_Options.png|center|frame|Figure 3: Layer Options]]
+[[image:TimEX_Tutorial_New_Layer_Options.png|center|frame|Figure 5: Layer Options]]
 Once your layer is loaded you need to repeat the same operation for the 3 other files.  Beside the name of the layers, all the other options are the same.