conda activate jbrowse cd jbrowse2 jbrowse add-assembly campy_data/genome_files/NC_002163.fa.gz --load inPlace --name NCTC11168 --displayName "Reference sequence (NCTC11168)" -t bgzipFasta # Annotation jbrowse add-track campy_data/annotation_files/NC_002163.gff.gz --load inPlace --name "Annotation" --category "Annotation files" --description "C. jejuni NCTC11168; Coordinates of ORFs, sRNAs and 5'UTRs" --overwrite jbrowse add-track campy_data/annotation_files/NC_002163_reannotation.gff.gz --load inPlace --name "Re-annotation" --category "Annotation files" --overwrite jbrowse add-track campy_data/annotation_files/NC_002163_novel.gff.gz --load inPlace --name "novel CJsORFs" --category "Annotation files" --overwrite jbrowse add-track campy_data/annotation_files/rbs_motif.gff.gz --load inPlace --name "RBS motif" --category "Annotation files" --overwrite jbrowse text-index --attributes Name,ID,locus_tag # TEX jbrowse add-track campy_data/coverage_files/TEX/TEX_minus_R1_fwd.bw --load inPlace --name "-TEX-R1 (fwd)" --category "dRNA-seq" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_minus_R1_fwd-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "dRNA-seq (mock-treated control)" --overwrite jbrowse add-track campy_data/coverage_files/TEX/TEX_minus_R1_rev.bw --load inPlace --name "-TEX-R1 (rev)" --category "dRNA-seq" --description "Coverage file Forward strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_minus_R1_rev-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "dRNA-seq (mock-treated control)" --overwrite jbrowse add-track campy_data/coverage_files/TEX/TEX_minus_R2_fwd.bw --load inPlace --name "-TEX-R2 (fwd)" --category "dRNA-seq" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_minus_R2_fwd-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "dRNA-seq (mock-treated control)" --overwrite jbrowse add-track campy_data/coverage_files/TEX/TEX_minus_R2_rev.bw --load inPlace --name "-TEX-R2 (rev)" --category "dRNA-seq" --description "Coverage file Forward strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_minus_R2_rev-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(190,190,190,1)", "negColor": "rgba(190,190,190,1)" }}}]}' --description "dRNA-seq (mock-treated control)" --overwrite jbrowse add-track campy_data/coverage_files/TEX/TEX_plus_R1_fwd.bw --load inPlace --name "+TEX-R1 (fwd)" --category "dRNA-seq" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_plus_R1_fwd-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --description "dRNA-seq (TEX-digested)" --overwrite jbrowse add-track campy_data/coverage_files/TEX/TEX_plus_R1_rev.bw --load inPlace --name "+TEX-R1 (rev)" --category "dRNA-seq" --description "Coverage file Forward strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_plus_R1_rev-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --description "dRNA-seq (TEX-digested)" --overwrite jbrowse add-track campy_data/coverage_files/TEX/TEX_plus_R2_fwd.bw --load inPlace --name "+TEX-R2 (fwd)" --category "dRNA-seq" --description "Coverage file Forward strand (+)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_plus_R2_fwd-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --description "dRNA-seq (TEX-digested)" --overwrite jbrowse add-track campy_data/coverage_files/TEX/TEX_plus_R2_rev.bw --load inPlace --name "+TEX-R2 (rev)" --category "dRNA-seq" --description "Coverage file Forward strand (-)." --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TEX_plus_R2_rev-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --description "dRNA-seq (TEX-digested)" --overwrite # Experiment 1 jbrowse add-track campy_data/coverage_files/E1/RNA-TruDWT-1.mil.forward.global.bw --load inPlace --name "Exp1-RNA-R1 (fwd)" --category "Exp1-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-TruDWT-1.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RNA-TruDWT-1.mil.reverse.global.bw --load inPlace --name "Exp1-RNA-R1 (rev)" --category "Exp1-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-TruDWT-1.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RNA-TruDWT-2.mil.forward.global.bw --load inPlace --name "Exp1-RNA-R2 (fwd)" --category "Exp1-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-TruDWT-2.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RNA-TruDWT-2.mil.reverse.global.bw --load inPlace --name "Exp1-RNA-R2 (rev)" --category "Exp1-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-TruDWT-2.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RNA-TruDWT-3.mil.forward.global.bw --load inPlace --name "Exp1-RNA-R3 (fwd)" --category "Exp1-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-TruDWT-3.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RNA-TruDWT-3.mil.reverse.global.bw --load inPlace --name "Exp1-RNA-R3 (rev)" --category "Exp1-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-TruDWT-3.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RIBO-TruDWT-1.mil.forward.global.bw --load inPlace --name "Exp1-RIBO-R1 (fwd)" --category "Exp1-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-TruDWT-1.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RIBO-TruDWT-1.mil.reverse.global.bw --load inPlace --name "Exp1-RIBO-R1 (rev)" --category "Exp1-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-TruDWT-1.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RIBO-TruDWT-2.mil.forward.global.bw --load inPlace --name "Exp1-RIBO-R2 (fwd)" --category "Exp1-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-TruDWT-2.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RIBO-TruDWT-2.mil.reverse.global.bw --load inPlace --name "Exp1-RIBO-R2 (rev)" --category "Exp1-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-TruDWT-2.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RIBO-TruDWT-3.mil.forward.global.bw --load inPlace --name "Exp1-RIBO-R3 (fwd)" --category "Exp1-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-TruDWT-3.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E1/RIBO-TruDWT-3.mil.reverse.global.bw --load inPlace --name "Exp1-RIBO-R3 (rev)" --category "Exp1-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-TruDWT-3.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite # Experiment 2 # Riboseq exp11-16 jbrowse add-track campy_data/coverage_files/E2/RNA-dcmeB-1.mil.forward.global.bw --load inPlace --name "Exp2-RNA-R1 (fwd)" --category "Exp2-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-dcmeB-1.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RNA-dcmeB-1.mil.reverse.global.bw --load inPlace --name "Exp2-RNA-R1 (rev)" --category "Exp2-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-dcmeB-1.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RNA-dcmeB-2.mil.forward.global.bw --load inPlace --name "Exp2-RNA-R2 (fwd)" --category "Exp2-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-dcmeB-2.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RNA-dcmeB-2.mil.reverse.global.bw --load inPlace --name "Exp2-RNA-R2 (rev)" --category "Exp2-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-dcmeB-2.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RNA-dcmeB-3.mil.forward.global.bw --load inPlace --name "Exp2-RNA-R3 (fwd)" --category "Exp2-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-dcmeB-3.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RNA-dcmeB-3.mil.reverse.global.bw --load inPlace --name "Exp2-RNA-R3 (rev)" --category "Exp2-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-dcmeB-3.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-1.mil.forward.global.bw --load inPlace --name "Exp2-RIBO-R1 (fwd)" --category "Exp2-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-1.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-1.mil.reverse.global.bw --load inPlace --name "Exp2-RIBO-R1 (rev)" --category "Exp2-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-1.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-2.mil.forward.global.bw --load inPlace --name "Exp2-RIBO-R2 (fwd)" --category "Exp2-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-2.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-2.mil.reverse.global.bw --load inPlace --name "Exp2-RIBO-R2 (rev)" --category "Exp2-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-2.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-3.mil.forward.global.bw --load inPlace --name "Exp2-RIBO-R3 (fwd)" --category "Exp2-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-3.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-3.mil.reverse.global.bw --load inPlace --name "Exp2-RIBO-R3 (rev)" --category "Exp2-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-3.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite # TIS(Ret) exp11-16 jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-1.mil.forward.threeprime31-32.bw --load inPlace --name "Exp2-RIBO-R1_3' (fwd)" --category "Exp2-TIS(Ret)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-1.mil.forward.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-1.mil.reverse.threeprime31-32.bw --load inPlace --name "Exp2-RIBO-R1_3' (rev)" --category "Exp2-TIS(Ret)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-1.mil.reverse.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-2.mil.forward.threeprime31-32.bw --load inPlace --name "Exp2-RIBO-R2_3' (fwd)" --category "Exp2-TIS(Ret)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-2.mil.forward.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-2.mil.reverse.threeprime31-32.bw --load inPlace --name "Exp2-RIBO-R2_3' (rev)" --category "Exp2-TIS(Ret)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-2.mil.reverse.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-3.mil.forward.threeprime31-32.bw --load inPlace --name "Exp2-RIBO-R3_3' (fwd)" --category "Exp2-TIS(Ret)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-3.mil.forward.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/RIBO-dcmeB-3.mil.reverse.threeprime31-32.bw --load inPlace --name "Exp2-RIBO-R3_3' (rev)" --category "Exp2-TIS(Ret)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-dcmeB-3.mil.reverse.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/TIS-dcmeB-1.mil.forward.threeprime31-32.bw --load inPlace --name "Exp2-TIS(Ret)-R1_3' (fwd)" --category "Exp2-TIS(Ret)" --description "TIS (Ret)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TIS-dcmeB-1.mil.forward.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/TIS-dcmeB-1.mil.reverse.threeprime31-32.bw --load inPlace --name "Exp2-TIS(Ret)-R1_3' (rev)" --category "Exp2-TIS(Ret)" --description "TIS (Ret)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TIS-dcmeB-1.mil.reverse.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/TIS-dcmeB-2.mil.forward.threeprime31-32.bw --load inPlace --name "Exp2-TIS(Ret)-R2_3' (fwd)" --category "Exp2-TIS(Ret)" --description "TIS (Ret)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TIS-dcmeB-2.mil.forward.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/TIS-dcmeB-2.mil.reverse.threeprime31-32.bw --load inPlace --name "Exp2-TIS(Ret)-R2_3' (rev)" --category "Exp2-TIS(Ret)" --description "TIS (Ret)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TIS-dcmeB-2.mil.reverse.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/TIS-dcmeB-3.mil.forward.threeprime31-32.bw --load inPlace --name "Exp2-TIS(Ret)-R3_3' (fwd)" --category "Exp2-TIS(Ret)" --description "TIS (Ret)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TIS-dcmeB-3.mil.forward.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E2/TIS-dcmeB-3.mil.reverse.threeprime31-32.bw --load inPlace --name "Exp2-TIS(Ret)-R1_3' (rev)" --category "Exp2-TIS(Ret)" --description "TIS (Ret)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "TIS-dcmeB-3.mil.reverse.threeprime31-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite # Riboseq exp28 jbrowse add-track campy_data/coverage_files/E3/RNA-A-1.mil.forward.global.bw --load inPlace --name "Exp3-RNA-R1 (fwd)" --category "Exp3-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-A-1.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RNA-A-1.mil.reverse.global.bw --load inPlace --name "Exp3-RNA-R1 (rev)" --category "Exp3-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-A-1.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RNA-A-2.mil.forward.global.bw --load inPlace --name "Exp3-RNA-R2 (fwd)" --category "Exp3-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-A-2.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RNA-A-2.mil.reverse.global.bw --load inPlace --name "Exp3-RNA-R2 (rev)" --category "Exp3-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-A-2.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RNA-A-3.mil.forward.global.bw --load inPlace --name "Exp3-RNA-R3 (fwd)" --category "Exp3-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-A-3.mil.forward.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RNA-A-3.mil.reverse.global.bw --load inPlace --name "Exp3-RNA-R3 (rev)" --category "Exp3-Ribo-seq" --description "total RNA-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RNA-A-3.mil.reverse.global-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(128,128,128,1)", "negColor": "rgba(128,128,128,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RIBO-A-1.mil.forward.global.bw --load inPlace --name "Exp3-RIBO-R1 (fwd)" --category "Exp3-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-A-1.mil.forward-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RIBO-A-1.mil.reverse.global.bw --load inPlace --name "Exp3-RIBO-R1 (rev)" --category "Exp3-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-A-1.mil.reverse-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RIBO-A-2.mil.forward.global.bw --load inPlace --name "Exp3-RIBO-R2 (fwd)" --category "Exp3-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-A-2.mil.forward-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RIBO-A-2.mil.reverse.global.bw --load inPlace --name "Exp3-RIBO-R2 (rev)" --category "Exp3-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-A-2.mil.reverse-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RIBO-A-3.mil.forward.global.bw --load inPlace --name "Exp3-RIBO-R3 (fwd)" --category "Exp3-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-A-3.mil.forward-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/RIBO-A-3.mil.reverse.global.bw --load inPlace --name "Exp3-RIBO-R3 (rev)" --category "Exp3-Ribo-seq" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "RIBO-A-3.mil.reverse-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite # TIS(Onc) exp28 jbrowse add-track campy_data/coverage_files/E3/tisonc_RIBO-R1.mil.forward.threeprime32.bw --load inPlace --name "Exp3-RIBO-R1_3' (fwd)" --category "Exp3-TIS(Onc)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_RIBO-R1.mil.forward.threeprime32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_RIBO-R1.mil.reverse.threeprime32.bw --load inPlace --name "Exp3-RIBO-R1_3' (rev)" --category "Exp3-TIS(Onc)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_RIBO-R1.mil.reverse.threeprime32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_RIBO-R2.mil.forward.threeprime32+33.bw --load inPlace --name "Exp3-RIBO-R2_3' (fwd)" --category "Exp3-TIS(Onc)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_RIBO-R2.mil.forward.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_RIBO-R2.mil.reverse.threeprime32+33.bw --load inPlace --name "Exp3-RIBO-R2_3' (rev)" --category "Exp3-TIS(Onc)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_RIBO-R2.mil.reverse.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_RIBO-R3.mil.forward.threeprime32+33.bw --load inPlace --name "Exp3-RIBO-R3_3' (fwd)" --category "Exp3-TIS(Onc)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_RIBO-R3.mil.forward.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_RIBO-R3.mil.reverse.threeprime32+33.bw --load inPlace --name "Exp3-RIBO-R3_3' (rev)" --category "Exp3-TIS(Onc)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_RIBO-R3.mil.reverse.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_TIS-R1.mil.forward.threeprime32.bw --load inPlace --name "Exp3-TIS(Onc)-R1_3' (fwd)" --category "Exp3-TIS(Onc)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_TIS-R1.mil.forward.threeprime32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_TIS-R1.mil.reverse.threeprime32.bw --load inPlace --name "Exp3-TIS(Onc)-R1_3' (rev)" --category "Exp3-TIS(Onc)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_TIS-R1.mil.reverse.threeprime32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_TIS-R2.mil.forward.threeprime32+33.bw --load inPlace --name "Exp3-TIS(Onc)-R2_3' (fwd)" --category "Exp3-TIS(Onc)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_TIS-R2.mil.forward.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_TIS-R2.mil.reverse.threeprime32+33.bw --load inPlace --name "Exp3-TIS(Onc)-R2_3' (rev)" --category "Exp3-TIS(Onc)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_TIS-R2.mil.reverse.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_TIS-R3.mil.forward.threeprime32+33.bw --load inPlace --name "Exp3-TIS(Onc)-R3_3' (fwd)" --category "Exp3-TIS(Onc)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_TIS-R3.mil.forward.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/tisonc_TIS-R3.mil.reverse.threeprime32+33.bw --load inPlace --name "Exp3-TIS(Onc)-R3_3' (rev)" --category "Exp3-TIS(Onc)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "tisonc_TIS-R3.mil.reverse.threeprime32+33-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite # TTS(Mono) exp28 jbrowse add-track campy_data/coverage_files/E3/ttsmono_RIBO-R1.mil.forward.threeprime29.bw --load inPlace --name "Exp3-RIBO-R1_3'_29nt (fwd)" --category "Exp3-TTS(Mono)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_RIBO-R1.mil.forward.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_RIBO-R1.mil.reverse.threeprime29.bw --load inPlace --name "Exp3-RIBO-R1_3'_29nt (rev)" --category "Exp3-TTS(Mono)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_RIBO-R1.mil.reverse.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_RIBO-R2.mil.forward.threeprime31+32.bw --load inPlace --name "Exp3-RIBO-R2_3'_31+32nt (fwd)" --category "Exp3-TTS(Mono)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_RIBO-R2.mil.forward.threeprime31+32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_RIBO-R2.mil.reverse.threeprime31+32.bw --load inPlace --name "Exp3-RIBO-R2_3'_31+32nt (rev)" --category "Exp3-TTS(Mono)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_RIBO-R2.mil.reverse.threeprime31+32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_RIBO-R3.mil.forward.threeprime30-32.bw --load inPlace --name "Exp3-RIBO-R3_3'_30-32nt (fwd)" --category "Exp3-TTS(Mono)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_RIBO-R3.mil.forward.threeprime30-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_RIBO-R3.mil.reverse.threeprime30-32.bw --load inPlace --name "Exp3-RIBO-R3_3'_30-32nt (rev)" --category "Exp3-TTS(Mono)" --description "Ribo-seq" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_RIBO-R3.mil.reverse.threeprime31+32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(0,0,0,1)", "negColor": "rgba(0,0,0,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TIS-R1.mil.forward.threeprime29.bw --load inPlace --name "Exp3-TIS(Onc)-R1_3'_29nt (fwd)" --category "Exp3-TTS(Mono)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TIS-R1.mil.forward.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TIS-R1.mil.reverse.threeprime29.bw --load inPlace --name "Exp3-TIS(Onc)-R1_3'_29nt (rev)" --category "Exp3-TTS(Mono)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TIS-R1.mil.reverse.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TIS-R2.mil.forward.threeprime31+32.bw --load inPlace --name "Exp3-TIS(Onc)-R2_3'_31+32nt (fwd)" --category "Exp3-TTS(Mono)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TIS-R1.mil.forward.threeprime31+32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TIS-R2.mil.reverse.threeprime31+32.bw --load inPlace --name "Exp3-TIS(Onc)-R2_3'_31+32nt (rev)" --category "Exp3-TTS(Mono)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TIS-R1.mil.reverse.threeprime31+32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TIS-R3.mil.forward.threeprime30-32.bw --load inPlace --name "Exp3-TIS(Onc)-R3_3'_30-32nt (fwd)" --category "Exp3-TTS(Mono)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TIS-R1.mil.forward.threeprime30-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TIS-R3.mil.reverse.threeprime30-32.bw --load inPlace --name "Exp3-TIS(Onc)-R3_3'_30-32nt (rev)" --category "Exp3-TTS(Mono)" --description "TIS (Onc)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TIS-R1.mil.reverse.threeprime30-32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(50,100,180,1)", "negColor": "rgba(50,100,180,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TTS-R1.mil.forward.threeprime29.bw --load inPlace --name "Exp3-TTS(Mono)-R1_3'_29nt (fwd)" --category "Exp3-TTS(Mono)" --description "TTS (Monosome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TTS-R1.mil.forward.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TTS-R1.mil.reverse.threeprime29.bw --load inPlace --name "Exp3-TTS(Mono)-R1_3'_29nt (rev)" --category "Exp3-TTS(Mono)" --description "TTS (Monosome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TTS-R1.mil.reverse.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TTS-R2.mil.forward.threeprime31+32.bw --load inPlace --name "Exp3-TTS(Mono)-R1_3'_31+32nt (fwd)" --category "Exp3-TTS(Mono)" --description "TTS (Monosome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TTS-R2.mil.forward.threeprime31+32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TTS-R2.mil.reverse.threeprime31+32.bw --load inPlace --name "Exp3-TTS(Mono)-R1_3'_31+32nt (rev)" --category "Exp3-TTS(Mono)" --description "TTS (Monosome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TTS-R2.mil.reverse.threeprime31+32-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TTS-R3.mil.forward.threeprime30-32.bw --load inPlace --name "Exp3-TTS(Mono)-R1_3'_30-32nt (fwd)" --category "Exp3-TTS(Mono)" --description "TTS (Monosome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TTS-R3.mil.forward.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsmono_TTS-R3.mil.reverse.threeprime30-32.bw --load inPlace --name "Exp3-TTS(Mono)-R1_3'_30-32nt (rev)" --category "Exp3-TTS(Mono)" --description "TTS (Monosome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsmono_TTS-R3.mil.reverse.threeprime29-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite # TTS(Di) exp28 jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R1.mil.forward.fiveprime58.bw --load inPlace --name "Exp3-TTS(Di)-R1_5' (fwd)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R1.mil.forward.fiveprime58-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R1.mil.reverse.fiveprime58.bw --load inPlace --name "Exp3-TTS(Di)-R1_5' (rev)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R1.mil.reverse.fiveprime58-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R2.mil.forward.fiveprime57+58.bw --load inPlace --name "Exp3-TTS(Di)-R2_5' (fwd)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R2.mil.forward.fiveprime57+58-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R2.mil.reverse.fiveprime57+58.bw --load inPlace --name "Exp3-TTS(Di)-R2_5' (rev)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R2.mil.reverse.fiveprime57+58-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R3.mil.forward.fiveprime58+59.bw --load inPlace --name "Exp3-TTS(Di)-R3_5' (fwd)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R3.mil.forward.fiveprime58+59-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R3.mil.reverse.fiveprime58+59.bw --load inPlace --name "Exp3-TTS(Di)-R3_5' (rev)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R3.mil.reverse.fiveprime58+59-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(120,30,75,1)", "negColor": "rgba(120,30,75,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R1.mil.forward.threeprime58.bw --load inPlace --name "Exp3-TTS(Di)-R1_3' (fwd)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R1.mil.forward.threeprime58-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(160,90,130,1)", "negColor": "rgba(160,90,130,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R1.mil.reverse.threeprime58.bw --load inPlace --name "Exp3-TTS(Di)-R1_3' (rev)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R1.mil.reverse.threeprime58-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(160,90,130,1)", "negColor": "rgba(160,90,130,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R2.mil.forward.threeprime59+60.bw --load inPlace --name "Exp3-TTS(Di)-R2_3' (fwd)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R2.mil.forward.threeprime59+60-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(160,90,130,1)", "negColor": "rgba(160,90,130,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R2.mil.reverse.threeprime59+60.bw --load inPlace --name "Exp3-TTS(Di)-R2_3' (rev)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R2.mil.reverse.threeprime59+60-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(160,90,130,1)", "negColor": "rgba(160,90,130,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R3.mil.forward.threeprime58+59.bw --load inPlace --name "Exp3-TTS(Di)-R3_3' (fwd)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R3.mil.forward.threeprime58+59-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(160,90,130,1)", "negColor": "rgba(160,90,130,1)" }}}]}' --overwrite jbrowse add-track campy_data/coverage_files/E3/ttsdi_TTS-R3.mil.reverse.threeprime58+59.bw --load inPlace --name "Exp3-TTS(Di)-R3_3' (rev)" --category "Exp3-TTS(Di)" --description "TTS (Disome)" --config '{"displays" : [ { "type": "LinearWiggleDisplay", "displayId": "ttsdi_TTS-R3.mil.reverse.threeprime58+59-LinearWiggleDisplay", "renderers" : { "XYPlotRenderer" : { "type": "XYPlotRenderer", "posColor" : "rgba(160,90,130,1)", "negColor": "rgba(160,90,130,1)" }}}]}' --overwrite