GeMoSeq - Revision history

Grau: /* Examples */

2025-11-18T16:08:56Z

Examples

← Older revision		Revision as of 16:08, 18 November 2025
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	== Examples ==		== Examples ==

	We give examples for applying GeMoSeq to a single sequencing library and for a larger-scale, integrated genome annotation together with GeMoMa [[GeMoSeq-Examples on a separate wiki page]].		We give examples for applying GeMoSeq to a single sequencing library and for a larger-scale, integrated genome annotation together with GeMoMa [[GeMoSeq-Examples\|on a separate wiki page]].

	== GeMoSeq ==		== GeMoSeq ==

Grau at 16:06, 18 November 2025

2025-11-18T16:06:59Z

← Older revision		Revision as of 16:06, 18 November 2025
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	The source code of GeMoSeq is available from the [https://github.com/Jstacs/Jstacs/tree/master/projects/gemoseq Jstacs GitHub repository].		The source code of GeMoSeq is available from the [https://github.com/Jstacs/Jstacs/tree/master/projects/gemoseq Jstacs GitHub repository].

			== Examples ==

			We give examples for applying GeMoSeq to a single sequencing library and for a larger-scale, integrated genome annotation together with GeMoMa [[GeMoSeq-Examples on a separate wiki page]].

	== GeMoSeq ==		== GeMoSeq ==

Grau: /* GeMoSeq */

2025-11-11T17:17:19Z

GeMoSeq

← Older revision		Revision as of 17:17, 11 November 2025
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	<tr style="vertical-align:top">		<tr style="vertical-align:top">
	<td><font color="green">threads</font></td>		<td><font color="green">threads</font></td>
	<td>The number of threads used for the tool, defaults to 1</td>		<td>The number of threads used for the tool, defaults to 1. Currently, I/O of GeMoSeq runs on a single thread and runtime is limited by I/O performance. Hence, running GeMoSeq with a large number of threads is not recommended. On our infrastructure, a number of 6 threads has been the sweet spot.</td>
	<td>INT</td>		<td>INT</td>
	</tr>		</tr>

Grau: /* GeMoSeq */

2025-11-11T17:15:04Z

GeMoSeq

← Older revision		Revision as of 17:15, 11 November 2025
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	<td>Maximum region length (Maximum length of a region considered before it is split, default = 750000)</td>		<td>Maximum region length (Maximum length of a region considered before it is split, default = 750000)</td>
	<td style="width:100px;">INT</td>		<td style="width:100px;">INT</td>
			</tr>
			<tr style="vertical-align:top">
			<td><font color="green">mrc</font></td>
			<td>Maximum region coverage (Maximum coverage in a region before reads are down-sampled, valid range = [0.0, Infinity], default = 100.0)</td>
			<td style="width:100px;">DOUBLE</td>
	</tr>		</tr>
	<tr style="vertical-align:top">		<tr style="vertical-align:top">
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	java -jar GeMoSeq-1.2.3.jar gemoseq g=<Genome> m=<Mapped_reads>		java -jar GeMoSeq-1.2.3.jar gemoseq g=<Genome> m=<Mapped_reads>


	== Predict CDS from GFF ==		== Predict CDS from GFF ==

Grau at 16:46, 11 November 2025

2025-11-11T16:46:31Z

Show changes

Grau: Grau moved page GeMoRNA to GeMoSeq

2025-11-11T16:00:50Z

Grau moved page GeMoRNA to GeMoSeq

← Older revision	Revision as of 16:00, 11 November 2025
(No difference)

Grau: /* Merge */

2025-05-28T07:00:16Z

Merge

← Older revision		Revision as of 07:00, 28 May 2025
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	''Merge'' may be called with		''Merge'' may be called with

	java -jar GeMoRNA-1.2.jar merge		java -jar GeMoRNA-1.2.1.jar merge

	and has the following parameters		and has the following parameters
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	'''Example:'''		'''Example:'''

	java -jar GeMoRNA-1.2.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>		java -jar GeMoRNA-1.2.1.jar merge g=<GeMoMa> GeMoRNA=<GeMoRNA>

	== Version history ==		== Version history ==

Grau: /* Predict CDS from GFF */

2025-05-28T07:00:06Z

Predict CDS from GFF

← Older revision		Revision as of 07:00, 28 May 2025
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	''Predict CDS from GFF'' may be called with		''Predict CDS from GFF'' may be called with

	java -jar GeMoRNA-1.2.jar predictCDS		java -jar GeMoRNA-1.2.1.jar predictCDS

	and has the following parameters		and has the following parameters
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	'''Example:'''		'''Example:'''

	java -jar GeMoRNA-1.2.jar predictCDS g=<Genome> p=<predicted_annotation>		java -jar GeMoRNA-1.2.1.jar predictCDS g=<Genome> p=<predicted_annotation>

	== Merge ==		== Merge ==

Grau: /* GeMoRNA */

2025-05-28T06:59:51Z

GeMoRNA

← Older revision		Revision as of 06:59, 28 May 2025
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	''GeMoRNA'' may be called with		''GeMoRNA'' may be called with

	java -jar GeMoRNA-1.2.jar gemorna		java -jar GeMoRNA-1.2.1.jar gemorna

	and has the following parameters		and has the following parameters
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	'''Example:'''		'''Example:'''

	java -jar GeMoRNA-1.2.jar gemorna g=<Genome> m=<Mapped_reads>		java -jar GeMoRNA-1.2.1.jar gemorna g=<Genome> m=<Mapped_reads>

	== Predict CDS from GFF ==		== Predict CDS from GFF ==

Grau: /* Command line tool */

2025-05-28T06:59:36Z

Command line tool

← Older revision		Revision as of 06:59, 28 May 2025
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	''GeMoRNA is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.''		''GeMoRNA is distributed in the hope that it will be useful, but without any warranty; without even the implied warranty of merchantability or fitness for a particular purpose.''

	GeMoRNA and auxiliary tools are packaged in one [http://www.jstacs.de/downloads/GeMoRNA-1.2.jar runnable JAR] that may be run from the command line with		GeMoRNA and auxiliary tools are packaged in one [http://www.jstacs.de/downloads/GeMoRNA-1.2.1.jar runnable JAR] that may be run from the command line with
	java -jar GeMoRNA-1.2.jar		java -jar GeMoRNA-1.2.1.jar

	which lists the tools available and usage information		which lists the tools available and usage information
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	merge - Merge		merge - Merge

	Syntax: java -jar GeMoRNA-1.2.jar <toolname> [<parameter=value> ...]		Syntax: java -jar GeMoRNA-1.2.1.jar <toolname> [<parameter=value> ...]

	Further info about the tools is given with		Further info about the tools is given with
	java -jar GeMoRNA-1.2.jar <toolname> info		java -jar GeMoRNA-1.2.1.jar <toolname> info

	For tests of individual tools:		For tests of individual tools:
	java -jar GeMoRNA-1.2.jar <toolname> test [<verbose>]		java -jar GeMoRNA-1.2.1.jar <toolname> test [<verbose>]

	Tool parameters are listed with		Tool parameters are listed with
	java -jar GeMoRNA-1.2.jar <toolname>		java -jar GeMoRNA-1.2.1.jar <toolname>

	You get a list of the tool parameters by calling GeMoRNA-1.2.jar with the corresponding tool name, e.g.,		You get a list of the tool parameters by calling GeMoRNA-1.2.1.jar with the corresponding tool name, e.g.,

	java -jar GeMoRNA-1.2.jar gemorna		java -jar GeMoRNA-1.2.1.jar gemorna

	The meaning of the individual tool parameters is described below.		The meaning of the individual tool parameters is described below.