JBrowse - Revision history

Dawes0011 at 09:01, 16 June 2023

2023-06-16T09:01:30Z

← Older revision		Revision as of 11:01, 16 June 2023
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	Download the latest JBrowse here: http://jbrowse.org/		Download the latest JBrowse here: http://jbrowse.org/

	Make a directory in <code>~~/cm~~/shared/apps/jbrowse/</code> for your species of interested (e.g. <code>mkdir Cyprinus_carpio</code>). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).		Make a directory in <code>/shared/apps/jbrowse/</code> for your species of interested (e.g. <code>mkdir Cyprinus_carpio</code>). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).
	Run the setup script to install perl dependencies and required modules		Run the setup script to install perl dependencies and required modules

Prins0891: to

 to fix code blocks

2023-06-15T14:47:25Z

<source> to <pre> to fix code blocks

← Older revision		Revision as of 16:47, 15 June 2023
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	Run the setup script to install perl dependencies and required modules		Run the setup script to install perl dependencies and required modules

	<~~source lang='bash'~~>		<pre>
	unzip JBrowse-1.12.0.zip		unzip JBrowse-1.12.0.zip
	mv JBrowse-1.12.0/* $PWD		mv JBrowse-1.12.0/* $PWD
	./setup.sh		./setup.sh
	</~~source~~>		</pre>

	=== Add reference sequence ===		=== Add reference sequence ===
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	Example code for chicken genome		Example code for chicken genome

	<~~source lang='bash'~~>		<pre>
	bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa		bin/prepare-refseqs.pl --fasta /lustre/nobackup/WUR/ABGC/shared/public_data_store/genomes/chicken/Ensembl74/Gallus_gallus.Galgal4.74.dna.toplevel.fa
	</~~source~~>		</pre>

	To remove tracks use following command:		To remove tracks use following command:

	<~~source lang='bash'~~>		<pre>
	bin/remove-track.pl -D --trackLabel 'trackname'		bin/remove-track.pl -D --trackLabel 'trackname'
	</~~source~~>		</pre>

	===Add annotation files (GFF/BED)===		===Add annotation files (GFF/BED)===
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	Add gene features:		Add gene features:

	<~~source lang='bash'~~>		<pre>
	bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3		bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3
	</~~source~~>		</pre>

	Add corresponding transcripts:		Add corresponding transcripts:

	<~~source lang='bash'~~>		<pre>
	bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3		bin/flatfile-to-json.pl --key "Transcripts" --className transcript --subfeatureClasses '{"exon": "exon", "CDS": "CDS", "five_prime_UTR": "five_prime_UTR", "three_prime_UTR": "three_prime_UTR"}' --config '{ "category": "GalGal4.83 Annotation" }' --type transcript --trackLabel Transcripts --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3
	</~~source~~>		</pre>

	===Alignment tracks (BAM)===		===Alignment tracks (BAM)===

	You can load single BAM-files by following command:		You can load single BAM-files by following command:
	<~~source lang='bash'~~>		<pre>
	bin/add-bam-track --label <label> --bam_url <url>		bin/add-bam-track --label <label> --bam_url <url>
	</~~source~~>		</pre>

	To load multiple BAM files present in a certain directory use:		To load multiple BAM files present in a certain directory use:
	<~~source lang='bash'~~>		<pre>

	for bam in /<dir>*.bam; do		for bam in /<dir>*.bam; do
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	done		done
	</~~source~~>		</pre>

	Make sure the BAM file can be read by a everybody if not use:		Make sure the BAM file can be read by a everybody if not use:
	<~~source lang='bash'~~>		<pre>
	chmod +r <BAM_file>		chmod +r <BAM_file>
	</~~source~~>		</pre>

	Make sure that all directoryies in the full path of the BAMfile are executable:		Make sure that all directoryies in the full path of the BAMfile are executable:
	<~~source lang='bash'~~>		<pre>
	chmod +x <dir>		chmod +x <dir>
	</~~source~~>		</pre>

	===Variant tracks (VCF)===		===Variant tracks (VCF)===
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	To load a VCF file in JBrowse make sure the file is gzipped and indexed		To load a VCF file in JBrowse make sure the file is gzipped and indexed

	<~~source lang='bash'~~>		<pre>
	tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz		tabix -p vcf Gallus_gallus_incl_consequences.vcf.gz

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	"type" : "HTMLVariants"		"type" : "HTMLVariants"
	} ' \| bin/add-track-json.pl data/trackList.json		} ' \| bin/add-track-json.pl data/trackList.json
	</~~source~~>		</pre>

	===Wiggle/BigWig tracks (WIG)===		===Wiggle/BigWig tracks (WIG)===

	You can load single BigWig-files by following command:		You can load single BigWig-files by following command:
	<~~source lang='bash'~~>		<pre>
	bin/add-bw-track --label <label> --bw_url <url>		bin/add-bw-track --label <label> --bw_url <url>
	</~~source~~>		</pre>

	===Evidence tracks===		===Evidence tracks===
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	Evidence tracks can be loaded in bed, gff and gbk format using		Evidence tracks can be loaded in bed, gff and gbk format using

	<~~source lang='bash'~~>		<pre>
	bin/flatfile-to-json.pl		bin/flatfile-to-json.pl
	</~~source~~>		</pre>

	Examples are given above.		Examples are given above.

Derks047: /* Add annotation files (GFF/BED) */

2019-11-25T09:33:55Z

Add annotation files (GFF/BED)

← Older revision		Revision as of 11:33, 25 November 2019
Line 45:		Line 45:

	<source lang='bash'>		<source lang='bash'>
	bin/flatfile-to-json.pl --key "~~Gene spans~~" ~~--className feature5~~ --type gene ~~--noSubfeatures~~ --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3		bin/flatfile-to-json.pl --key "Genes" --type gene --config '{ "category": "GalGal4.83 Annotation" }' --trackLabel Genes --gff ../ensembl_data/Gallus_gallus.Galgal4.83.gff3
	</source>		</source>

Derks047: /* Wiggle/BigWig tracks (WIG) */

2017-03-07T15:19:57Z

Wiggle/BigWig tracks (WIG)

← Older revision		Revision as of 17:19, 7 March 2017
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	You can load single BigWig-files by following command:		You can load single BigWig-files by following command:
	<source lang='bash'>		<source lang='bash'>
	bin/add-bw-track --label <label> --~~bam_url~~ <url>		bin/add-bw-track --label <label> --bw_url <url>
	</source>		</source>

Derks047: /* Wiggle/BigWig tracks (WIG) */

2017-03-07T15:19:03Z

Wiggle/BigWig tracks (WIG)

@@ Line 123: / Line 123: @@
 You can load single BigWig-files by following command:
 <source lang='bash'>
-bin/add-bam-track --label <label> --bam_url <url>
+bin/add-bw-track --label <label> --bam_url <url>
 </source>

Megen002: /* Install JBrowse */

2016-12-16T13:03:21Z

Install JBrowse

← Older revision		Revision as of 15:03, 16 December 2016
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	<source lang='bash'>		<source lang='bash'>
	unzip JBrowse-1.12.0.zip		unzip JBrowse-1.12.0.zip
	cd JBrowse-1.12.0		mv JBrowse-1.12.0/* $PWD
	./setup.sh		./setup.sh
	</source>		</source>

Megen002: /* Typical commands used to set up a JBrowse */

2016-12-16T12:56:54Z

Typical commands used to set up a JBrowse

← Older revision		Revision as of 14:56, 16 December 2016
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	** https://jbrowse.hpcagrogenomics.wur.nl/cattle/		** https://jbrowse.hpcagrogenomics.wur.nl/cattle/
	** https://jbrowse.hpcagrogenomics.wur.nl/turkey/		** https://jbrowse.hpcagrogenomics.wur.nl/turkey/
			** https://jbrowse.hpcagrogenomics.wur.nl/Cyprinus_carpio/
	* Users are free to add usefull commands to this tutorial		* Users are free to add usefull commands to this tutorial

Megen002: /* Install JBrowse */

2016-12-16T12:13:40Z

Install JBrowse

← Older revision		Revision as of 14:13, 16 December 2016
Line 14:		Line 14:
	Download the latest JBrowse here: http://jbrowse.org/		Download the latest JBrowse here: http://jbrowse.org/

	Make a directory in <code>/cm/shared/apps/jbrowse/</code> for your species of interested (e.g. Cyprinus_carpio). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).		Make a directory in <code>/cm/shared/apps/jbrowse/</code> for your species of interested (e.g. <code>mkdir Cyprinus_carpio</code>). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).
	Run the setup script to install perl dependencies and required modules		Run the setup script to install perl dependencies and required modules

Megen002: /* Install JBrowse */

2016-12-16T12:13:04Z

Install JBrowse

← Older revision		Revision as of 14:13, 16 December 2016
Line 14:		Line 14:
	Download the latest JBrowse here: http://jbrowse.org/		Download the latest JBrowse here: http://jbrowse.org/

			Make a directory in <code>/cm/shared/apps/jbrowse/</code> for your species of interested (e.g. Cyprinus_carpio). Move the downloaded JBrowse source files there. All further procedures detailed in this Wiki page assume working from that directory (NOTE: if your species of interest is already there, contact the maintainer of that JBrowse instance).
	Run the setup script to install perl dependencies and required modules		Run the setup script to install perl dependencies and required modules

Megen002: /* Install JBrowse */

2016-12-16T12:08:54Z

Install JBrowse

← Older revision		Revision as of 14:08, 16 December 2016
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	<source lang='bash'>		<source lang='bash'>
	unzip JBrowse-1.12.0.zip		unzip JBrowse-1.12.0.zip
			cd JBrowse-1.12.0
	./setup.sh		./setup.sh
	</source>		</source>