Tracks and Tables

Methylation Data

Methylation Data was exported to the following formats:

Sample summary

This section contains summary metrics for each sample as well as links to exported files. The summary table below contains the following metrics. It is also available as csv file.

Bed files for each sample contain the locations of methylation sites and regions the methylation level (in the score column). The following table links to the files. The files can be quite large in size, so you might want to consider using the "save as" option instead of opening the links directly.

sampleName sites_bigBedFile tiling_bigBedFile genes_bigBedFile promoters_bigBedFile cpgislands_bigBedFile sites_bedFile tiling_bedFile genes_bedFile promoters_bedFile cpgislands_bedFile sites_num sites_covgMean sites_covgMedian sites_covgPerc25 sites_covgPerc75 sites_numCovg5 sites_numCovg10 sites_numCovg30 sites_numCovg60 tiling_num tiling_covgMean tiling_covgMedian tiling_covgPerc25 tiling_covgPerc75 tiling_numCovg5 tiling_numCovg10 tiling_numCovg30 tiling_numCovg60 tiling_numSitesMean tiling_numSitesMedian tiling_numSites2 tiling_numSites5 tiling_numSites10 tiling_numSites20 genes_num genes_covgMean genes_covgMedian genes_covgPerc25 genes_covgPerc75 genes_numCovg5 genes_numCovg10 genes_numCovg30 genes_numCovg60 genes_numSitesMean genes_numSitesMedian genes_numSites2 genes_numSites5 genes_numSites10 genes_numSites20 promoters_num promoters_covgMean promoters_covgMedian promoters_covgPerc25 promoters_covgPerc75 promoters_numCovg5 promoters_numCovg10 promoters_numCovg30 promoters_numCovg60 promoters_numSitesMean promoters_numSitesMedian promoters_numSites2 promoters_numSites5 promoters_numSites10 promoters_numSites20 cpgislands_num cpgislands_covgMean cpgislands_covgMedian cpgislands_covgPerc25 cpgislands_covgPerc75 cpgislands_numCovg5 cpgislands_numCovg10 cpgislands_numCovg30 cpgislands_numCovg60 cpgislands_numSitesMean cpgislands_numSitesMedian cpgislands_numSites2 cpgislands_numSites5 cpgislands_numSites10 cpgislands_numSites20
Human|EWS_FLI1_low|NA|1 Human|EWS_FLI1_low|NA|1 bigBed bigBed bigBed bigBed bigBed bed bed bed bed bed 20345706 5.78879808840254 4 3 7 10075643 2610463 216859 22363 566840 207.820411403571 136 75 247 564524 561563 535550 465915 35.7862086914928 28 565621 558405 524407 392805 51260 1634.87182988685 315 36 1751 48969 45976 39713 35301 267.119531977131 47 47594 41177 36262 31581 56170 268.3692896564 123 53 354 55451 54385 49003 40367 33.5271632620632 22 55608 52549 44671 31125 27059 486.047969252374 321 136 656 26942 26741 25905 24317 52.9566349928459 37 26998 26768 26024 21322
Human|EWS_FLI1_low|NA|2 Human|EWS_FLI1_low|NA|2 bigBed bigBed bigBed bigBed bigBed bed bed bed bed bed 20253204 6.66071590450578 5 3 8 11505113 3896353 267648 29289 566956 237.98671854606 145 75 284 564542 561249 532326 462868 35.6234876408604 27 565738 558670 523314 386967 51178 1891.04314353824 374 43 2015 48926 46383 40648 36389 266.256139950994 47 47523 41197 36222 31570 56236 305.218845579344 146 57 412 55437 54267 49100 41653 33.3104927699995 22 55667 52396 44460 30967 27053 556.553580009611 374 172 743 26952 26795 26182 25201 53.0292768830025 37 26982 26734 25928 21375
Human|EWS_FLI1_high|NA|1 Human|EWS_FLI1_high|NA|1 bigBed bigBed bigBed bigBed bigBed bed bed bed bed bed 20285273 7.73357139438054 6 3 10 12902857 5351561 398351 43209 567034 276.719357216675 166 84 329 564667 561636 536561 476172 35.6800076673091 27 565787 558809 523454 388236 51232 2215.91025140537 428 49 2376.25 49253 46914 41514 37270 266.724903603244 47 47537 41177 36227 31587 56249 367.944727906274 168 66 483 55457 54477 49890 43346 33.3340277900387 22 55661 52371 44495 30987 27031 682.139099552366 446 201 914 26943 26765 26226 25405 53.2886597938144 37 26959 26697 25953 21351
Human|EWS_FLI1_high|NA|2 Human|EWS_FLI1_high|NA|2 bigBed bigBed bigBed bigBed bigBed bed bed bed bed bed 20136851 7.39821707972115 6 3 9 12105556 4799102 399458 50047 566927 262.833068455022 152 75 310 564328 560728 530071 461512 35.418825002462 27 565692 558600 522016 383917 51167 2109.99155705826 413 47 2258 48987 46470 41073 36920 264.862841187532 47 47561 41124 36159 31536 56225 346.174264117386 160 60 471 55427 54220 49123 42232 33.1238016207913 22 55648 52363 44338 30803 27017 643.028759669838 436 202 850 26914 26774 26239 25398 52.923432512749 37 26935 26651 25939 21350

Tracks Hubs

Track Hub data was generated for export to various genome browsers. Note that you need a server that is capable of serving the tracks to the genome browser via URL. Below, instructions are provided to view the tracks in the UCSC genome browser. Of course the files can also be viewed in other browsers such as the Ensembl genome browser.

  1. Make sure you are viewing this report via the internet and not locally (simply look at the URL in the address line of your browser). If this is not the case, copy the files belonging to this report to a directory which is accessible via the internet and enter the corresponding URL in your browser. If you don't want to copy the entire report, it suffices to copy the track hub directories (see table(s) below).
  2. Make sure the hg19 subdirectories in the track hub directory (for its location be referred to the table(s) below) contain all the required bigBed/bigWig files
  3. Go to the UCSC hub connection website to the "My Hubs" tab and add the web-URL of the hub.txt file in the directory you just copied. Hint: You can use the copy link functionality of your browser (right mouse click) on the track hub txt column in the table(s) below. Don't forget to click on "Load Selected Hubs".
  4. Make sure you are looking at the correct genome (hg19). The loaded hubs should now appear below the browsing window where you can modify their display settings.
More information on UCSC track hubs can be found here. Below, you find table(s) containing the directory names for the bed/bedGraph and track hub directories for all exported data, site and region types.

bigBed

bigWig