JBrowse - Revision history

Rf at 07:08, 4 August 2017

2017-08-04T07:08:51Z

2017-07-20T12:35:37Z

2017-07-06T13:27:07Z

2017-07-06T12:50:09Z

2017-06-21T11:25:56Z

2017-06-20T16:48:42Z

2017-06-16T10:10:49Z

2017-06-16T09:53:16Z

2017-06-16T09:51:30Z

2017-06-16T09:26:51Z

@@ Line 15: / Line 15: @@
 * Available as subdir within apache root dir
-The zeroth step can seem somewhat tedious and unnecessary , but it is best to follow it, for completeness sake. A file called setup.sh exisits in the root directory of the JBrowse (note: not the bin directory where all the other scripts are kept). Run this first.
+The very first, or zeroth step can seem somewhat tedious and unnecessary, but it is best to follow it, for completeness sake.
 Then, get reference sequence up

@@ Line 3: / Line 3: @@
 JBrowse is a genome browser which is web-based (as opposed to genome browsers such as Artemis and IGV which are stand-alone applications).
-It was designed as a fast version of GBrowse,the well-known web-based UCSD genome browser. The key to its speed is Javascript language in which it was developed and which explains the '''J''' in its name.
+It was designed as a fast version of GBrowse,the well-known web-based UCSD genome browser. The key to its speed is the Javascript language in which it was developed and which explains the '''J''' in its name.
 = Using =
@@ Line 15: / Line 15: @@
 * Available as subdir within apache root dir
-First get reference sequence up
+The zeroth step can seem somewhat tedious and unnecessary , but it is best to follow it, for completeness sake. A file called setup.sh exisits in the root directory of the JBrowse (note: not the bin directory where all the other scripts are kept). Run this first.
   bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa

← Older revision		Revision as of 13:27, 6 July 2017
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	bin/add-bam-track.pl --label WTIPbam --bam_url WTIP_srtd.bam		bin/add-bam-track.pl --label WTIPbam --bam_url WTIP_srtd.bam
		+
		+	However, to get a clean and approachable coverage track in reads per 100bp, you need to use bigWig files, so a prior operation of converting BAM to bigWig (bw) files is necessary using deeptools:
		+
		+	bamCoverage -b reads.bam -o coverage.bw
		+
		+	Then we can go ahead and:
		+
		+	bin/add-bw-track.pl --plot --bw_url ULSINP_srtd_cov.bw --label ULS1INPcov
		+
		+	Probably you will need to edit the trackList.json file to color these.

	Adding a bed6+4 file characteristic of MACS2 peak-calling narrowPeak format.		Adding a bed6+4 file characteristic of MACS2 peak-calling narrowPeak format.

← Older revision		Revision as of 12:50, 6 July 2017
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	bin/add-bam-track.pl --label WTIPbam --bam_url WTIP_srtd.bam		bin/add-bam-track.pl --label WTIPbam --bam_url WTIP_srtd.bam
		+
		+	Adding a bed6+4 file characteristic of MACS2 peak-calling narrowPeak format.
		+
		+	bin/flatfile-to-json.pl --trackLabel WTpeaks --trackType CanvasFeatures --bed data/wtip_pk.npk --clientConfig '{"featureCss": "background-color: #668; height: 8px;"}'

	= Links =		= Links =

@@ Line 33: / Line 33: @@
 = Links =
 * The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface.
 * The new official JBrowse [http://gmod.org/wiki/JBrowse_FAQ FAQ].
 * Using JBrowse will mean knowing your file formats, so [https://genome.ucsc.edu/FAQ/FAQformat.html here] is UCSC's definitions.

← Older revision		Revision as of 16:48, 20 June 2017
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	* The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface.		* The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface.
	* The new official JBrowse [http://gmod.org/wiki/JBrowse_FAQ FAQ].		* The new official JBrowse [http://gmod.org/wiki/JBrowse_FAQ FAQ].
		+	* Using JBrowse will mean knowing your file formats, so [https://genome.ucsc.edu/FAQ/FAQformat.html here] is UCSC's definitions.

← Older revision		Revision as of 10:10, 16 June 2017
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	= Links =		= Links =
	* The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface.		* The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface.
		+	* The new official JBrowse [http://gmod.org/wiki/JBrowse_FAQ FAQ].

@@ Line 19: / Line 19: @@
   bin/prepare-refseqs.pl --fasta ~/scafs0/eelScaffold32.fa
-Then it will accept GFF£ files (not GTF) files as feature tracks with this command:
+Then it will accept GFF3 files (not GTF) files as feature tracks with this command:
   bin/flatfile-to-json.pl --gff ~/scafs0/aug_s32_lp.gff --trackType CanvasFeatures --trackLabel aug_lp_s32
-If you have files in GTF, you can convert them to GFF3 with, say, Agustus' script in the following way:
+If you happen to have files in GTF, you can convert them to GFF3 with, say, Augustus' script in the following way:
   ~/swmake/augustus-3.2.2/scripts/gtf2gff.pl --printExon --gff3 < aug_s320_lp.gtf --out=aug_s320_lp.gff
 = Links =
 * The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface.

← Older revision		Revision as of 09:51, 16 June 2017
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	~/swmake/augustus-3.2.2/scripts/gtf2gff.pl --printExon --gff3 < aug_s320_lp.gtf --out=aug_s320_lp.gff		~/swmake/augustus-3.2.2/scripts/gtf2gff.pl --printExon --gff3 < aug_s320_lp.gtf --out=aug_s320_lp.gff
		+
		+	= Links =
		+	* The 2016 [https://genomebiology.biomedcentral.com/articles/10.1186/s13059-016-0924-1 Genome Biology paper] describing JBrowse, with a good description of the user interface.

@@ Line 1: / Line 1: @@
 =Introduction=
-Quick Javascript based Genome Viewer
+JBrowse is a genome browser which is web-based (as opposed to genome browsers such as Artemis and IGV which are stand-alone applications).
 = Using =
@@ Line 9: / Line 11: @@
 * Beside the magnifying glass icon, one can just the scaffolds one would liek seelcted as main reference sequence.
-= Install =
+= Installation notes =
 * Available as subdir within apache root dir