Mercurial > repos > fubar > jbrowse2

comparison jbrowse2.xml @ 5:efc64d8f4b72 draft

Find changesets by keywords (author, files, the commit message), revision number or hash, or revset expression.
planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit 79e81bef99f582680d9aa4eec88980c675f3fae9
author fubar
date Tue, 09 Jan 2024 05:24:48 +0000
parents 2de9f585505b
children b04fd993b31e
comparison
equal deleted inserted replaced
4:54396f0323f4 5:efc64d8f4b72
995 995
996 **Track Groups** represent a set of tracks in a single category. These 996 **Track Groups** represent a set of tracks in a single category. These
997 can be used to let your users understand relationships between large 997 can be used to let your users understand relationships between large
998 groups of tracks. 998 groups of tracks.
999 999
1000 .. image:: sections.png
1001
1002 Annotation Tracks 1000 Annotation Tracks
1003 ----------------- 1001 -----------------
1004 1002
1005 There are a few different types of tracks supported, each with their own 1003 There are a few different types of tracks supported, each with their own
1006 set of options: 1004 set of options:
1009 ~~~~~~~~ 1007 ~~~~~~~~
1010 1008
1011 These are standard feature tracks. They usually highlight genes, 1009 These are standard feature tracks. They usually highlight genes,
1012 mRNAs and other features of interest along a genomic region. 1010 mRNAs and other features of interest along a genomic region.
1013 1011
1012 When these contain tens of millions of features, such as repeat regions from a VGP assembly, displaying one at a time leads
1013 to extremely slow loading times when a large region is in view, unless the "LinearPileupDisplay" display option is
1014 selected for that track in the styling options section. The default is LinearBasicDisplay, which shows all details and works
1015 well for relatively sparse bed files.
1016
1014 BAM Pileups 1017 BAM Pileups
1015 ~~~~~~~~~~~ 1018 ~~~~~~~~~~~
1016 1019
1017 We support BAM files and can automatically generate SNP tracks based on 1020 We support BAM files and can automatically generate SNP tracks based on
1018 that bam data. 1021 that bam data.
1019 1022
1020 1023
1021 BlastXML 1024 BlastXML
1022 ~~~~~~~~ 1025 ~~~~~~~~
1023
1024 .. image:: blast.png
1025 1026
1026 JiG now supports both blastn and blastp datasets. JiG internally uses a 1027 JiG now supports both blastn and blastp datasets. JiG internally uses a
1027 blastXML to gapped GFF3 tool to convert your blastxml datasets into a 1028 blastXML to gapped GFF3 tool to convert your blastxml datasets into a
1028 format amenable to visualization in JBrowse. This tool is also 1029 format amenable to visualization in JBrowse. This tool is also
1029 available separately from the IUC on the toolshed. 1030 available separately from the IUC on the toolshed.
1042 10 hits or so. 1043 10 hits or so.
1043 1044
1044 **Protein blast search** option merely informs underlying tools that 1045 **Protein blast search** option merely informs underlying tools that
1045 they should adjust feature locations by 3x. 1046 they should adjust feature locations by 3x.
1046 1047
1047 Bigwig XY
1048 ~~~~~~~~~
1049
1050 .. image:: bigwig.png
1051
1052
1053 1048
1054 VCFs/SNPs 1049 VCFs/SNPs
1055 ~~~~~~~~~ 1050 ~~~~~~~~~
1056 1051
1057 These tracks do not support any special configuration. 1052 These tracks do not support any special configuration.