Jbrowse染色体片段的显示的配置方法

来源：互联网发布：php限制ip访问次数编辑：程序博客网时间：2024/05/16 06:40

使用gff3格式的数据，通过jbrowse自带的perl脚本进行转化，具体命令实例如下所示：

bin/flatfile-to-json.pl --gff data_files/小鼠.GRCm38.78.gff --trackType CanvasFeatures --out sample_data/json/Guinea_pigs --trackLabel Guinea_pigs

flatfile-to-json.pl \
( --gff <GFF3 file> | --bed <BED file> | --gbk <GenBank file> ) \
--trackLabel <track identifier> \
[ --trackType <JS Class> ] \
[ --out <output directory> ] \
[ --key <human-readable track name> ] \
[ --className <CSS class name for displaying features> ] \
[ --urltemplate "http://example.com/idlookup?id={id}" ] \
[ --arrowheadClass <CSS class> ] \
[ --noSubfeatures ] \
[ --subfeatureClasses '{ JSON-format subfeature class map }' ] \
[ --clientConfig '{ JSON-format style configuration for this track }' ] \
[ --config '{ JSON-format extra configuration for this track }' ] \
[ --thinType <BAM -thin_type> ] \
[ --thicktype <BAM -thick_type>] \
[ --type <feature types to process> ] \
[ --nclChunk <chunk size for generated NCLs> ] \
[ --compress ] \
[ --sortMem <memory in bytes to use for sorting> ] \
[ --maxLookback <maximum number of features to buffer in gff3 files> ] \
[ --nameAttributes "name,alias,id" ]

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