Documentation - Revision history

Julien: /* Select Coordinate System */

2014-06-27T20:13:38Z

‎Select Coordinate System

2014-06-26T19:43:34Z

‎Using Tracks

2014-06-26T18:20:30Z

‎DNA Sequence Layer Operations

2014-06-26T18:19:21Z

‎DNA Sequence Layer Operations

2014-06-26T18:18:54Z

‎DNA Sequence Layer Operations

2014-06-26T16:02:01Z

‎Show Statistics

2014-06-26T16:00:47Z

‎Common operations

2014-06-26T15:47:12Z

‎CG Methylation Profile

2014-06-26T15:46:48Z

‎CG Methylation Profile

2014-06-26T15:30:13Z

‎Repeat Layer Operations

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 ===== Select Coordinate System =====
 [[image:mg_coordinate_chooser.png|left|thumb|150px|Coordinate System chooser]]
-The coordinate system of GenPlay can be changed by selecting one on the list located on the bottom right of the main frame. The default system is the one of the Meta Genome; the Reference Genome coordinate system is also available. The user can also choose the one of any of the loaded genome. This does not affect operation, only the red position numbers on the top of the frame as well as the position search bar on the bottom.
+The coordinate system of GenPlay can be changed by selecting one on the list located on the bottom right of the main frame. The default system is the one of the Meta Reference Genome; the Reference Genome coordinate system is also available. The user can also choose the one of any of the loaded genome. This does not affect operation, only the red position numbers on the top of the frame as well as the position search bar on the bottom.
 ===== Multi-Genome Project Properties =====

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 [[image:paste_layer.png|right|thumb|200px|Track Menu]]
 To copy layers, select the desired track where the layers are and click on the copy option in the contextual menu or press CTRL+C.
 To cut layers, select the desired track where the layers are and click on the cut option in the contextual menu or press CTRL+X.
@@ Line 922: / Line 923: @@
 To paste a track, select the track where you want to paste and click on the paste option in the contextual menu or press CTRL+P.
-A new window will appear showing all layers recently copied/cut that can be pasted on the track. The user has to select all layers he wants to paste and then click "Ok".
+A track can be pasted into a text file in which case the data of the active layer will be pasted as text (the pasted text will be limited to the genomic range currently displayed). It can be pasted in an image editor in which case an image of the track will be pasted. It can also be pasted in a file explorer in which case the layer will be saved as a GPTF (GenPlay Track File) or pasted in an other GenPlay track in which case the copied layers will be added to the track.
 ==== Taking a Screenshot of the Track ====
 To take a screenshot, select a track and choose the "Save as Image" option in the contextual menu.
 ==== Using the Undo / Redo / Reset Options ====

← Older revision		Revision as of 18:20, 26 June 2014
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	=== DNA Sequence Layer Operations ===		=== DNA Sequence Layer Operations ===
		+
		+	==== Compare Sequences ====
	This operation takes two sequence layer in input and generate a variable window layer showing the differences between the two sequence layers. For each position where the sequences are different the result layer will show a window of 1bp with the following score:		This operation takes two sequence layer in input and generate a variable window layer showing the differences between the two sequence layers. For each position where the sequences are different the result layer will show a window of 1bp with the following score:

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 {|
-! Nucleotide of the 1st layer ! Nucleotide of the 2nd layer ! Score
+! Nucleotide of the 1st layer
 |-
 | A

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 === DNA Sequence Layer Operations ===
-There is currently no operation available for the sequence layers.
+This operation takes two sequence layer in input and generate a variable window layer showing the differences between the two sequence layers. For each position where the sequences are different the result layer will show a window of 1bp with the following score:
 === Mask Layer Operations ===

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 ===== Show Statistics =====
-Shows the minimum, maximum, average scores per chromosome and genome wide. Also show the number of windows, the sum of the length of windows with a non zero score and the sum of the scores (normalized by the windows length).
+Shows the minimum, maximum, average scores per chromosome and genome wide. Also shows the number of windows, the sum of the window lengths with a non zero score and the sum of the scores (normalized by the window lengths).
 ===== Filter =====

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 ===== Standard Score =====
 Calculates the standard score for the selected layer i.e. (x - avg) / stdev; where x is the score, avg is the average score of the layer and stdev is the standard deviation of the scores of the layer.
 ===== Filter =====

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 This operation computes the methylation values on CG sequences by combining the value on the C position and the value on the G position.
-The result is a list of windows covering the CG sequences and having the sum of the scores on the C and on the G base.
+The result is a list of windows covering the CG sequences and having the sum of the score on the C and the score on the G base.
 This is based on data fron a sequence layer in order to find CG sequences.

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 === Repeat Layer Operations ===
-There is currently no operation available for the repeat layer.
 === DNA Sequence Layer Operations ===