Difference between revisions of "PAG2024 bash script"

Latest revision as of 22:04, 9 January 2024

#!/bin/bash

jbrowse create public_html --force 

cd public_html

jbrowse add-assembly data/c_elegans.PRJNA13758.WS286.genomic.fa.gz \
         --displayName "C. elegans N2" \
         --name c_elegans_PRJNA13758 \
         --type bgzipFasta \
         --load inPlace \
         --refNameAliases data/ce_aliases.txt

jbrowse add-track data/c_elegans.genes.sorted.gff3.gz \
         --name Genes \
         --description "Curated genes from WormBase" \
         --load inPlace \
         --config '{ "metadata": { "source":"GFF3 created by Scott Cain, from WormBase annotation file at https://downloads.wormbase.org/releases/WS286/species/c_elegans/PRJNA13758/c_elegans.PRJNA13758.WS286.annotations.gff3.gz" } }'

jbrowse text-index --attributes=Name,ID,locus --tracks c_elegans.genes.sorted.gff3

jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS286/c_elegans_PRJNA13758/tracks/Curated%20Genes%20\(protein%20coding\)/{refseq}/trackData.jsonz \
   --name "Protein coding genes" \
   --description "Only protein coding genes from WormBase" \
   --config '{ "metadata": { "source":"Directly from WormBases JBrowse 1 instance at https://wormbase.org/tools/genome/jbrowse" } }'


jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/CeNDR/CB4854.bam \
       --name "CeNDR BAM" \
       --config '{ "metadata": { "source":"Used by permission from http://elegansvariation.org/" } }'

jbrowse add-track https://storage.googleapis.com/elegansvariation.org/releases/current/WI.current.soft-filtered.vcf.gz \
         --name Variants \
         --config '{ "metadata": { "source":"Used by permission from http://elegansvariation.org/" } }'

jbrowse add-track https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw \
   --name "Frame 1 usage" \
   --config '{ "metadata": { "source":"Publicly available data from the Broad Institute: https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/mm39/PhyloCSF_raw.html" } }'

jbrowse add-track-json '{"type":"MultiQuantitativeTrack","trackId":"multiwiggle_phylo","name":"Forward PhyloCSF","assemblyNames":["c_elegans_PRJNA13758"],"adapter":{"type":"MultiWiggleAdapter","bigWigs":["https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+1.bw","https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+2.bw","https://data.broadinstitute.org/compbio1/PhyloCSFtracks/ce11/latest/PhyloCSF+3.bw"]},"metadata":{"source":"Publicly available data from the Broad Institute: https://data.broadinstitute.org/compbio1/PhyloCSFtracks/trackHub/mm39/PhyloCSF_raw.html"},"displays":[{"type":"MultiLinearWiggleDisplay","displayId":"multiwiggle_phylo-MultiLinearWiggleDisplay"}]}'

jbrowse add-assembly data/c_briggsae.PRJNA10731.WS287.genomic.fa.gz \
        --displayName "C. briggsae" \
        --name c_briggsae_PRJNA10731 \
        --type bgzipFasta \
        --load inPlace

jbrowse make-pif data/c_elegans.c_briggsae.paf

jbrowse add-track c_elegans.c_briggsae.pif.gz \
     --assemblyNames c_briggsae_PRJNA10731,c_elegans_PRJNA13758 \
     --description "A minimap2 comparison of C. elegans and C. briggsae" \
     --load inPlace \
     --name "C. elegans/C. briggsae Synteny" \
     --config '{ "metadata": { "source":"Comparative analysis using this command: minimap2 -c data/c_elegans.PRJNA13758.WS286.genomic.fa.gz data/c_briggsae.PRJNA10731.WS287.genomic.fa.gz > c_elegans.c_briggsae.paf" } }'


jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/WS287/c_briggsae_PRJNA10731/tracks/Curated_Genes/{refseq}/trackData.jsonz \
     --assemblyNames c_briggsae_PRJNA10731 \
     --name "C. briggsae Genes" \
     --trackId c_briggsae_genes \
     --config '{ "metadata": { "source":"Curated genes track directly from the WormBase JBrowse 1 instance." } }'

jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/maroilley/candidateSV.vcf.gz \
       --name "Structural Variant Candidates VCF" \
       --assemblyNames c_elegans_PRJNA13758 \
       --category "Structural Variants"

jbrowse add-track https://s3.amazonaws.com/agrjbrowse/MOD-jbrowses/WormBase/static_tracks/modencode-bucket/test/maroilley/VC109_Het_trim_bwaMEM_sort.bam \
       --name "VC109 BAM" \
       --assemblyNames c_elegans_PRJNA13758 \
       --category "Structural Variants"