Jbrowse生成json文件步骤

Submitted by admin on Sat, 12/14/2024 - 08:31

####测试！初步success

#在/var/www/html/Artocarpus/JBrowse-1.16.11目录下执行

bin/prepare-refseqs.pl --fasta /opt/download/genomeData/FE/FE.genome.fasta --out ArtocarpusData/json/FE

bin/flatfile-to-json.pl --out ArtocarpusData/json/FE --gff /opt/download/genomeData/FE/FE.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead

#浏览器显示

http://10.26.13.151/Artocarpus/jbrowse/?loc=FE06%3A10713171..10721880&tr...

 

#我的浏览器显示完全：tracklist=0作用：控制是否显示轨道列表（Track List）。nav=1作用：控制是否显示导航工具（Navigation）。overview=0作用：控制是否显示全基因组概览（Overview）。

 

http://10.26.13.151/Artocarpus/jbrowse/index.html?data=ArtocarpusData%2Fjson%2FFE&loc=FE011%3A2301223..20731067&tracks=DNA%2Cgenes&tracklist=1&nav=1&overview=1&highlight=

#YJY完全：

http://varnatech.cn/shrimpPortal/jbrowse/index.html?data=shrimpData%2Fjson%2FHar&loc=NW_024757794.1%3A9714718..9799126&tracks=DNA%2Cgenes&tracklist=1&nav=1&overview=1&highlight=

#00Runprepare-refseqs.sh

bin/prepare-refseqs.pl --fasta /data/upload/genomeData/97103_genome_v2.fa --out icugi_data_v2/json/cvu
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/BottleGourd_HZ_v2.fa --out icugi_data_v2/json/lhg
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/Cargyrosperma_v2.chr.fa --out icugi_data_v2/json/car
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/Chayote_genome.fa --out icugi_data_v2/json/sed
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/ChineseLong_genome_v3.fa --out icugi_data_v2/json/ccl
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/CM4.0_PacBio.fasta --out icugi_data_v2/json/cmd
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/Cmaxima_genome_v1.1.fa --out icugi_data_v2/json/cma
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/c_metuliferus_genome.fa --out icugi_data_v2/json/cme
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/Cmoschata_genome_v1.fa --out icugi_data_v2/json/cmo
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/colocynthis_v1.chr.fa --out icugi_data_v2/json/col

#01Runflatfile-to-json.sh

bin/flatfile-to-json.pl --out icugi_data_v2/json/cvu --gff /data/upload/genomeData/97103_gene_gff_v2.final.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/lhg --gff /data/upload/genomeData/BottleGourd_HZ_v2.final.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/car --gff /data/upload/genomeData/Cargyrosperma_v2.chr.final.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/sed --gff /data/upload/genomeData/Chayote_gene.final.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/ccl --gff /data/upload/genomeData/ChineseLong_gene_v3.final.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/cmd --gff /data/upload/genomeData/CM4.0_parse.final.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/cma --gff /data/upload/genomeData/Cmaxima_gene_v1.1.final.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead

#0202Rungenerate-names.sh

bin/generate-names.pl --out icugi_data_v2/json/cvu
bin/generate-names.pl --out icugi_data_v2/json/lhg
bin/generate-names.pl --out icugi_data_v2/json/car
bin/generate-names.pl --out icugi_data_v2/json/sed
bin/generate-names.pl --out icugi_data_v2/json/ccl
bin/generate-names.pl --out icugi_data_v2/json/cmd
bin/generate-names.pl --out icugi_data_v2/json/cma
bin/generate-names.pl --out icugi_data_v2/json/cme

#03updateJBrowse.sh

bin/prepare-refseqs.pl --fasta /data/upload/genomeData/genome/AG-4_genome.fa --out icugi_data_v2/json/lac
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/genome/DHL92_genome_v4.fa --out icugi_data_v2/json/cmd
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/genome/HZ_genome_v2.fa --out icugi_data_v2/json/lhg
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/genome/L_cylindrica_genome.fa --out icugi_data_v2/json/lcy
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/genome/OHB3-1_genome_v2.fa --out icugi_data_v2/json/moh
bin/prepare-refseqs.pl --fasta /data/upload/genomeData/genome/Qingpiguo_genome.fa --out icugi_data_v2/json/sgr

bin/flatfile-to-json.pl --out icugi_data_v2/json/lac --gff /data/upload/genomeData/AG-4_genome.fa --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/cmd --gff /data/upload/genomeData/DHL92_v4.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/lhg --gff /data/upload/genomeData/HZ_v2.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/lcy --gff /data/upload/genomeData/L_cylindrica.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/moh --gff /data/upload/genomeData/OHB3-1_v2.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/sgr --gff /data/upload/genomeData/Qingpiguo.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead

bin/generate-names.pl --out icugi_data_v2/json/lac
bin/generate-names.pl --out icugi_data_v2/json/cmd
bin/generate-names.pl --out icugi_data_v2/json/lhg
bin/generate-names.pl --out icugi_data_v2/json/lcy
bin/generate-names.pl --out icugi_data_v2/json/moh
bin/generate-names.pl --out icugi_data_v2/json/sgr

#04RunAddAhrd2gff.sh

bin/flatfile-to-json.pl --out icugi_data_v2/json/bhi --gff /data/upload/genomeData/gffwAHRD/WG_AHRD.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/cag --gff /data/upload/genomeData/gffwAHRD/IVF77_AHRD.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/cam --gff /data/upload/genomeData/gffwAHRD/USVL246_v1_AHRD.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/car --gff /data/upload/genomeData/gffwAHRD/Cargyrosperma_AHRD_v2.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead
bin/flatfile-to-json.pl --out icugi_data_v2/json/ccg --gff /data/upload/genomeData/gffwAHRD/WCG_AHRD_v2.5.gff3 --type mRNA --autocomplete all --trackLabel genes --key 'Gene models' --getSubfeatures --className transcript --trackType CanvasFeatures --subfeatureClasses '{"CDS": "transcript-CDS", "exon": "hidden"}' --arrowheadClass arrowhead