Catchitt - Revision history

Grau: /* Version history */

2021-10-07T20:51:46Z

Version history

← Older revision		Revision as of 20:51, 7 October 2021
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	== Version history ==		== Version history ==
			* Catchitt v0.1.4: Fixing a bug that lead to an Exception if chromosomes did not appear in lexicographical order in the input files

	* Catchitt v0.1.3: Bugfix to load Catchitt classifiers learned with older Catchitt versions		* [http://www.jstacs.de/downloads/Catchitt-0.1.3.jar Catchitt v0.1.3]: Bugfix to load Catchitt classifiers learned with older Catchitt versions

	* [http://www.jstacs.de/downloads/~~Catchitt_0~~.1.2.jar Catchitt v0.1.2]: Bugfixes, new experimental tools for handling methylation levels		* [http://www.jstacs.de/downloads/Catchitt-0.1.2.jar Catchitt v0.1.2]: Bugfixes, new experimental tools for handling methylation levels

	* [http://www.jstacs.de/downloads/Catchitt_0.1.1.jar Catchitt v0.1.1]: Bugfixes for border cases; reduced debugging output		* [http://www.jstacs.de/downloads/Catchitt_0.1.1.jar Catchitt v0.1.1]: Bugfixes for border cases; reduced debugging output

	* Catchitt v0.1: [http://www.jstacs.de/downloads/Catchitt_0.1.jar Initial release]		* Catchitt v0.1: [http://www.jstacs.de/downloads/Catchitt_0.1.jar Initial release]

2021-10-07T20:49:03Z

Downloads

← Older revision		Revision as of 20:49, 7 October 2021
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	''Catchitt 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.''		''Catchitt 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.''

	* [http://www.jstacs.de/downloads/Catchitt-0.1.3.jar JAR download]		* [http://www.jstacs.de/downloads/Catchitt-0.1.4.jar JAR download]
	* the source code of Catchitt is available from [https://github.com/Jstacs/Jstacs github] in package projects.encodedream.		* the source code of Catchitt is available from [https://github.com/Jstacs/Jstacs github] in package projects.encodedream.
	* [http://www.jstacs.de/downloads/motifs.tgz motifs] used in the ENCODE-DREAM challenge		* [http://www.jstacs.de/downloads/motifs.tgz motifs] used in the ENCODE-DREAM challenge

2021-10-07T20:48:49Z

Usage

← Older revision		Revision as of 20:48, 7 October 2021
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	== Usage ==		== Usage ==

	In the following <code>Catchitt.jar</code> stands for the Catchitt binary in its current version, which currently would be 0.1.3. So every occurrence of <code>Catchitt.jar</code> needs to be replaced by <code>Catchitt-0.1.3.jar</code> when running code examples with the current Catchitt binary version.		In the following <code>Catchitt.jar</code> stands for the Catchitt binary in its current version, which currently would be 0.1.4. So every occurrence of <code>Catchitt.jar</code> needs to be replaced by <code>Catchitt-0.1.4.jar</code> when running code examples with the current Catchitt binary version.

2020-10-13T19:43:14Z

Version history

← Older revision		Revision as of 19:43, 13 October 2020
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	== Version history ==		== Version history ==

	* Catchitt v0.1.2: Bugfixes, new experimental tools for handling methylation levels		* Catchitt v0.1.3: Bugfix to load Catchitt classifiers learned with older Catchitt versions

			* [http://www.jstacs.de/downloads/Catchitt_0.1.2.jar Catchitt v0.1.2]: Bugfixes, new experimental tools for handling methylation levels

	* [http://www.jstacs.de/downloads/Catchitt_0.1.1.jar Catchitt v0.1.1]: Bugfixes for border cases; reduced debugging output		* [http://www.jstacs.de/downloads/Catchitt_0.1.1.jar Catchitt v0.1.1]: Bugfixes for border cases; reduced debugging output

	* Catchitt v0.1: [http://www.jstacs.de/downloads/Catchitt_0.1.jar Initial release]		* Catchitt v0.1: [http://www.jstacs.de/downloads/Catchitt_0.1.jar Initial release]

2020-10-13T19:41:24Z

Downloads

← Older revision		Revision as of 19:41, 13 October 2020
Line 17:		Line 17:
	''Catchitt 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.''		''Catchitt 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.''

	* [http://www.jstacs.de/downloads/Catchitt.jar JAR download]		* [http://www.jstacs.de/downloads/Catchitt-0.1.3.jar JAR download]
	* the source code of Catchitt is available from [https://github.com/Jstacs/Jstacs github] in package projects.encodedream.		* the source code of Catchitt is available from [https://github.com/Jstacs/Jstacs github] in package projects.encodedream.
	* [http://www.jstacs.de/downloads/motifs.tgz motifs] used in the ENCODE-DREAM challenge		* [http://www.jstacs.de/downloads/motifs.tgz motifs] used in the ENCODE-DREAM challenge

2020-10-13T19:41:10Z

Usage

← Older revision		Revision as of 19:41, 13 October 2020
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	== Usage ==		== Usage ==

			In the following <code>Catchitt.jar</code> stands for the Catchitt binary in its current version, which currently would be 0.1.3. So every occurrence of <code>Catchitt.jar</code> needs to be replaced by <code>Catchitt-0.1.3.jar</code> when running code examples with the current Catchitt binary version.


	Catchitt can be started by calling		Catchitt can be started by calling

2020-10-05T11:58:05Z

Version history

← Older revision		Revision as of 11:58, 5 October 2020
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	== Version history ==		== Version history ==

	* Catchitt v0.1.1: Bugfixes for border cases; reduced debugging output		* Catchitt v0.1.2: Bugfixes, new experimental tools for handling methylation levels

			* [http://www.jstacs.de/downloads/Catchitt_0.1.1.jar Catchitt v0.1.1]: Bugfixes for border cases; reduced debugging output

	* Catchitt v0.1: [http://www.jstacs.de/downloads/Catchitt_0.1.jar Initial release]		* Catchitt v0.1: [http://www.jstacs.de/downloads/Catchitt_0.1.jar Initial release]

2020-10-05T11:55:39Z

Tools

@@ Line 163: / Line 163: @@
   java -jar Catchitt.jar access d="Bigwig" i=fold_enrich.bw f=hg19.fa.fai b=50 outdir=dnase
 === Motif scores ===
@@ Line 401: / Line 443: @@
   java -jar Catchitt.jar predict c=cls/Classifiers.xml a=dnase/Chromatin_accessibility.tsv.gz m=motif1/Motif_scores.tsv.gz m=motif2/Motif_scores.tsv.gz f=hg19.fa.fai p="chr8,chr21" abb=1 aba=4 n=3 outdir=predict
 == Standard pipeline ==

2020-10-05T11:53:35Z

Usage

← Older revision		Revision as of 11:53, 5 October 2020
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	access - Chromatin accessibility		access - Chromatin accessibility
			methyl - Methylation levels
	motif - Motif scores		motif - Motif scores
	labels - Derive labels		labels - Derive labels

2019-02-23T22:36:15Z

Using DNase-seq BAM files and multiple motifs

← Older revision		Revision as of 22:36, 23 February 2019
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	java -jar Catchitt.jar access i=fibroblasts/ENCFF368XNE.bam b=50 outdir=fibroblasts/access_bam/		java -jar Catchitt.jar access i=fibroblasts/ENCFF368XNE.bam b=50 outdir=fibroblasts/access_bam/

	We also compute the motif-based features from the additional motif files. For the PWM model of SP1, we switch the input format but still use the low-memory version of "motif" that we also used for the HOCOMOCO PWM:		We also compute the motif-based features from the additional motif files. For the PWM model of SP1, we switch the input format to Dimont XMLs but still use the low-memory version of "motif" that we also used for the HOCOMOCO PWM:

	java -jar Catchitt.jar motif d=motifs/SP1/ENCSR000BHK_SP1-human_1_hg19-model-2.xml\		java -jar Catchitt.jar motif d=motifs/SP1/ENCSR000BHK_SP1-human_1_hg19-model-2.xml\