Bambus Manual - Revision history

Dmb000006: /* Untangling scaffolds */

2011-01-07T15:02:20Z

‎Untangling scaffolds

2011-01-07T14:58:00Z

2011-01-07T14:49:54Z

Making an entry for the .lib file and correcting a within page link to that entry.

2011-01-07T14:48:11Z

‎.dot file

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-The test.untangle.xml file has the same format as the output file ([[#.out.xml|.out.xml]]) and for each scaffold (e.g. scaff_1) contains one or more unambiguous scaffolds called "scaff_1_1, scaff_1_2, etc". You can use the [[#Getting more (or less) information from the output|printScaff]] command to process the untangled file the same way you would process a normal Bambus output.
+The test.untangle.xml file has the same format as the output file ([[#.out.xml|.out.xml]]) and for each scaffold (e.g. scaff_1) contains one or more unambiguous scaffolds called "scaff_1_1, scaff_1_2, etc". You can use the [[printScaff]] command to process the untangled file the same way you would process a normal Bambus output.
-−
-−
 == File formats ==

← Older revision		Revision as of 14:58, 7 January 2011
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	BAMBUS was written by Mihai Pop and Dan Kosack.		BAMBUS was written by Mihai Pop and Dan Kosack.
		+
		+
		+	[[Category:Bambus]]

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 * [[#.evidence.xml|test.evidence.xml]] - XML representation of all the linking evidence provided.
 * [[#.out.xml|test.out.xml]] - XML representation of the scaffolds.
-* [[#.ps file|test.lib]] - list of the codes associated with each input library. These codes are reported on the links in the output file. <!-- The link here looks wrong! -->
+* [[#.lib file|test.lib]] - list of the codes associated with each input library. These codes are reported on the links in the output file. <!-- The link here looks wrong! -->
 * [[#.sum file|test.sum]] - one-line sumaries of all scaffolds.
 * [[#.oo file|test.oo]] - order and orientation information for all the contigs.
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-If you are uncertain of which libraries your project uses, run Bambus without a configuration file. The libraries will be listed in a file ending in ".libs".
+If you are uncertain of which libraries your project uses, run Bambus without a configuration file. The libraries will be listed in a file ending in "[[#.lib file|.libs]]".

← Older revision		Revision as of 14:48, 7 January 2011
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	Represents a graphical representation of the scaffolds in GraphViz format. Please see the [http://www.research.att.com/sw/tools/graphviz/ AT&T GraphViz] website for more information on this file format.		Represents a graphical representation of the scaffolds in GraphViz format. Please see the [http://www.research.att.com/sw/tools/graphviz/ AT&T GraphViz] website for more information on this file format.

		+	=== .lib file ===
		+	Lists the libraries and their internal ID's

	=== .ps file ===		=== .ps file ===