diff --git a/trackHub/trackDb.txt b/trackHub/trackDb.txt deleted file mode 100644 index 4beaad412e..0000000000 --- a/trackHub/trackDb.txt +++ /dev/null @@ -1,239 +0,0 @@ -# m6A tracks -track m6A -compositeTrack on -shortLabel m6A -longLabel m6A -type bigBed 12 + -maxItems 100000 - - track m6A_pat - parent m6A - bigDataUrl bb/2.m6a.bb - shortLabel m6A_pat - longLabel m6A_pat - type bigBed 12 + - itemRgb on - visibility dense - - track m6A_mat - parent m6A - bigDataUrl bb/1.m6a.bb - shortLabel m6A_mat - longLabel m6A_mat - type bigBed 12 + - itemRgb on - visibility dense - - track m6A_unk - parent m6A - bigDataUrl bb/unk.m6a.bb - shortLabel m6A_unk - longLabel m6A_unk - type bigBed 12 + - itemRgb on - visibility dense - -# cpg tracks -track CpG -compositeTrack on -shortLabel CpG -longLabel CpG -type bigWig 0 1000 -maxItems 100000 -maxHeightPixels 50:50:1 -autoScale off -viewLimits 0.0:100.0 -alwaysZero on - - track cpg_mat - parent CpG - bigDataUrl bw/canu-plus-whatshap-maternal.cpg-proportion.bw - shortLabel cpg_mat - longLabel cpg_mat - type bigWig - visibility full - - track cpg_pat - parent CpG - bigDataUrl bw/canu-plus-whatshap-paternal.cpg-proportion.bw - shortLabel cpg_pat - longLabel cpg_pat - type bigWig - visibility full - - track cpg_unk - parent CpG - bigDataUrl bw/canu-plus-whatshap-unknown.cpg-proportion.bw - shortLabel cpg_unk - longLabel cpg_unk - type bigWig - visibility full - - - -# Peak calls -track FDRpeaks -compositeTrack on -shortLabel FDRpeaks -longLabel FDRpeaks -type bigBed 9 + -maxItems 100000 - - track FDRpeaks97 - parent FDRpeaks - bigDataUrl bb/peaks.Phased_GM12878_all.FDR97.2010365224.bb - shortLabel FDRpeaks97 - longLabel FDRpeaks97 - type bigBed 3 - visibility hide - - track FDRpeaks_10_percent - parent FDRpeaks - bigDataUrl bb/peaks.GM12878_130X_10_percent.bb - shortLabel FDRpeaks_10_percent - longLabel FDRpeaks_10_percent - type bigBed 3 - visibility dense - - -# Codependency Interact Track -track Codependency -type bigInteract -visibility full -shortLabel Codependency -longLabel Codependency interact track -itemRgb on -scoreMin 175 -maxHeightPixels 300:150:20 -bigDataUrl bb/interact_track_GM12878.bb - -# GM12878 TSS - CAGE + Gencode v42 -track TSS -compositeTrack on -shortLabel TSS -longLabel TSS CAGE + Gencode v42 -type bigBed 6 -maxItems 100000 - - track TSS_CAGE - parent TSS - bigDataUrl bb/cage_gencode42_TSS_intersect_formatted.bb - shortLabel TSS_CAGE - longLabel TSS CAGE + Gencode v42 - type bigBed 6 - itemRgb on - visibility dense - -# GM12878 CTCF Peak Paternal Xi Actuation % -track CTCF_Xi -compositeTrack on -shortLabel CTCF_Xi -longLabel CTCF Peak Paternal Xi Actuation -type bigBed 6 -maxItems 100000 - - track CTCF_Xi_Act - parent CTCF_Xi - bigDataUrl bb/color-coded_CTCF_pat_act.bb - shortLabel CTCF_Xi_Act - longLabel CTCF Peak Paternal Xi - type bigBed 6 - spectrum on - visibility dense - -# GM12878 CTCF Peak Paternal Xi Actuation % -track TSS_escape -compositeTrack on -shortLabel TSS_escape -longLabel TSS Fiber-seq Escape Status -type bigBed 9 -maxItems 100000 - - track TSS_escape_color - parent TSS_escape - bigDataUrl bb/color-coded_X_TSS.bb - shortLabel TSS_escape_color - longLabel CTSS Escape Status - type bigBed 9 - itemRgb on - visibility dense - -# GM12878 CTCF footprinting color-coded by Xi -track Xi_CTCF -compositeTrack on -shortLabel Xi_CTCF_footprints_color -longLabel Xi CTCF footprints color-coded -type bigBed 9 -maxItems 100000 - - track Xi_CTCF_footprint_color - parent Xi_CTCF - bigDataUrl bb/GM12878_Xi_CTCF_footprints.bb - shortLabel Xi_CTCF_footprints_color - longLabel Xi CTCF footprints color-coded - type bigBed 9 - itemRgb on - visibility dense - - -# more tracks - - - -# cpg tracks -track new_FIRE_FDR -compositeTrack on -shortLabel new_FIRE_FDR -longLabel new_FIRE_FDR -type bigWig -maxItems 100000 -maxHeightPixels 100:100:1 -alwaysZero on - - track log_fdr - parent new_FIRE_FDR - bigDataUrl bw/log_FDR.bw - shortLabel log_fdr - longLabel log_fdr - type bigWig - autoScale on - visibility full - yLineOnOff on - yLineMark 20 - gridDefault on - - - track fire_score - parent new_FIRE_FDR - bigDataUrl bw/score.bw - shortLabel fire_score - longLabel fire_score - type bigWig - autoScale on - viewLimits 0.0:100.0 - visibility full - - - track log_fdr_low_cov - parent new_FIRE_FDR - bigDataUrl bw/log_FDR_low.bw - shortLabel log_fdr_low_cov - longLabel log_fdr_low_cov - type bigWig - autoScale on - visibility full - yLineOnOff on - yLineMark 20 - gridDefault on - - - track fire_score_low_cov - parent new_FIRE_FDR - bigDataUrl bw/score_low.bw - shortLabel fire_score_low_cov - longLabel fire_score_low_cov - type bigWig - autoScale on - viewLimits 0.0:100.0 - visibility full -