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comparison jbrowse2.xml @ 107:a074cd6b5905 draft

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planemo upload for repository https://github.com/galaxyproject/tools-iuc/tree/master/tools/jbrowse2 commit a1537aea75fc902d0e38c0b7c698830a939648b1-dirty
author fubar
date Sun, 23 Jun 2024 06:59:56 +0000
parents dc3fe98e7b37
children 5d1259b88c27
comparison
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106:0082924757b0 107:a074cd6b5905
1147 1147
1148 1148
1149 Use and local viewing 1149 Use and local viewing
1150 ===================== 1150 =====================
1151 1151
1152 All tracks have a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks. 1152 Browser tracks need a coordinate system, based on the reference genome, so that must be chosen before adding groups of tracks.
1153 There are 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been 1153
1154 At present, 10 Galaxy datatypes that can be turned into a track for display - in all cases, the selected reference genome must have been
1154 used to generate the data: 1155 used to generate the data:
1155 1156
1156 bam 1157 bam
1157 bed 1158 bed
1158 bigwig 1159 bigwig
1162 hic 1163 hic
1163 maf 1164 maf
1164 paf 1165 paf
1165 vcf 1166 vcf
1166 1167
1167 cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. 1168 Note that cram and bam will be large, so very slow amd are only recommended if you need the cigar annotation. Otherwise conversion to bed is recommended to slim them down.
1168 Otherwise conversion to bed is recommended to slim them down.
1169 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended. 1169 Unfortunately if you have millions of rows in a bed, it will also be very slow - in which case a bigwig is recommended.
1170 1170
1171 A JBrowse2 history item can be opened by viewing it (the "eye" icon). 1171 A JBrowse2 history item can be opened by viewing it (the "eye" icon).
1172 1172
1173 Overview 1173 Overview