[{"type":"bedGraph","name":"DAC plus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DAC.CTSS.normalized.plus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0.5,"thmax":2,"thpercentile":90,"height":30,"summeth":1},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"DAC minus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DAC.CTSS.normalized.minus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":-2,"thmax":-0.5,"thpercentile":90,"height":30,"summeth":1},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"DACSB plus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DACSB.CTSS.normalized.plus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0.5,"thmax":2,"thpercentile":90,"height":30,"summeth":2},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"DACSB minus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DACSB.CTSS.normalized.minus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":-2,"thmax":-0.5,"thpercentile":90,"height":30,"summeth":1},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"DZNEP plus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DZNEP.CTSS.normalized.plus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0.5,"thmax":2,"thpercentile":90,"height":30,"summeth":2},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"DZNEP minus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DZNEP.CTSS.normalized.minus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":-2,"thmax":-0.5,"thpercentile":90,"height":30,"summeth":1},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"DMSO plus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DMSO.CTSS.normalized.plus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0.5,"thmax":2,"thpercentile":90,"height":30,"summeth":2},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"DMSO minus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/DMSO.CTSS.normalized.minus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":-2,"thmax":-0.5,"thpercentile":90,"height":30,"summeth":1},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"SAHA plus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/SAHA.CTSS.normalized.plus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0.5,"thmax":2,"thpercentile":90,"height":30,"summeth":2},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"SAHA minus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/SAHA.CTSS.normalized.minus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":-2,"thmax":-0.5,"thpercentile":90,"height":30,"summeth":1},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"SB939 plus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/SB939.CTSS.normalized.plus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":0.5,"thmax":2,"thpercentile":90,"height":30,"summeth":2},"custom_annotation":["bedGraph"]},{"type":"bedGraph","name":"SB939 minus TPM","url":"https://cgs.wustl.edu/~jli/CAGE_lj/SB939.CTSS.normalized.minus.bedGraph1.gz","mode":1,"qtc":{"anglescale":1,"pr":153,"pg":0,"pb":0,"nr":255,"ng":0,"nb":0,"pth":"#ffff00","nth":"#800000","thtype":1,"thmin":-2,"thmax":-0.5,"thpercentile":90,"height":30,"summeth":1},"custom_annotation":["bedGraph"]},{"type":"BAM","name":"DMSO PE-CAGE Alignment","url":"https://cgs.wustl.edu/~dli/CAGE/PE/DMSO_Aligned.out_unique.bam","mode":3,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"#000000","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"forwardcolor":"rgb(0,0,153)","reversecolor":"rgb(153,0,0)","mismatchcolor":"rgb(255,255,0)"}},{"type":"native_track","list":[{"name":"refGene","mode":3,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"rgb(0,0,0)","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"bedcolor":"rgb(0,77,153)"}},{"name":"rmsk_all","mode":7,"defaultmode":7,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"#000000","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"bedcolor":"#336666","scorescalelst":[{"type":0},{"type":0}]},"showscoreidx":2,"scorenamelst":["Smith-Waterman score","SW score normalized by length","1-divergence%"],"scorescalelst":[{"type":0},{"type":0},{"type":0}],"categories":{"1":["SINE - short interspersed nuclear element","#cc0000"],"2":["LINE - long interspersed nuclear element","#FF6600"],"3":["LTR - long terminal repeat element","#006600"],"4":["DNA transposon","#4A72E8"],"5":["Simple repeat, micro-satellite","#AB833B"],"6":["Satellite repeat","#660000"],"7":["Low complexity repeat","#663333"],"8":["RNA repeat","#cc33ff"],"9":["Other repeats","#488E8E"],"10":["Unknown","#5C5C5C"],"-1":["no information","transparent"]}},{"name":"gencodeV17","mode":3,"qtc":{"anglescale":1,"pr":0,"pg":77,"pb":0,"nr":0,"ng":0,"nb":230,"pth":"#800000","nth":"#000099","thtype":0,"thmin":0,"thmax":10,"thpercentile":95,"height":50,"summeth":1,"textcolor":"rgb(0,0,0)","fontsize":"8pt","fontfamily":"sans-serif","fontbold":false,"bedcolor":"rgb(0,77,153)"},"categories":{"1":["coding","rgb(0,60,179)"],"2":["non-coding","rgb(0,128,0)"],"3":["pseudogene","rgb(230,0,172)"],"4":["problem","rgb(255,0,0)"],"5":["polyA","rgb(0,0,51)"],"-1":["no information","transparent"]}}]},{"type":"BAM","name":"DAC PE-CAGE Alignment","url":"https://cgs.wustl.edu/~dli/CAGE/PE/DAC_Aligned.out_unique.bam","mode":"hide","qtc":{}},{"type":"BAM","name":"DZNEP PE-CAGE Alignment","url":"https://cgs.wustl.edu/~dli/CAGE/PE/DZNEP_Aligned.out_unique.bam","mode":"hide","qtc":{}},{"type":"BAM","name":"SAHA PE-CAGE Alignment","url":"https://cgs.wustl.edu/~dli/CAGE/PE/SAHA_Aligned.out_unique.bam","mode":"hide","qtc":{}},{"type":"BAM","name":"SB939 PE-CAGE Alignment","url":"https://cgs.wustl.edu/~dli/CAGE/PE/SB939_Aligned.out_unique.bam","mode":"hide","qtc":{}},{"type":"BAM","name":"DACSB PE-CAGE Alignment","url":"https://cgs.wustl.edu/~dli/CAGE/PE/DACSB_Aligned.out_unique.bam","mode":"hide","qtc":{}},{"type":"coordinate_override","coord":"chr12,31689587,chr12,31824060"},{"type":"metadata","vocabulary":{"Sample":["DMSO","DZNEP","DAC","SAHA","SB939","DACSB"],"Assay/Method":["CAGEr"],"Data format":["BED","bigWig","bedGraph","interaction","categorical","methylC","Hammock","BAM"]},"show":["Sample","Assay/Method"],"source":"https://cgs.wustl.edu/~jli/CAGE_lj/CAGE_norm.json","termname":{},"termcolor":{},"termdesc":{}}]