Converting BED files to Read Density Signal Tracks

  1. Go to http://www.genboree.org
  2. Log in if necessary
  3. Click on the 'Workbench' tab or directly visit the Workbench http://genboree.org/java-bin/workbench.jsp
  4. Click the 'Databases' tab in the top Genboree Menu Bar
  5. Click 'Create Database'
  6. Select the Group in which you would like to create the Database
  7. Select your 'Reference Sequence' (i.e. 'Template: Human (HG19))' or leave this as '** User Will Upload **' if you do not know your Reference Sequence or do not plan on utilizing one
  8. Enter a Database name into the Database' text area
  9. Click 'Create'
  10. Expand the Group that contains your Database of interest
  11. Expand 'Databases'
  12. Drag your Database into the 'Output Targets' window
  13. Drag your target database from the 'Data Selector' window over into the 'Output Targets' window
  14. Select the 'Data' tab, the 'Files' tab, and then the 'Transfer File' tab
  15. Click the 'Choose File' button and select the file you wish to upload
  16. If you are uploading a multi-file archive (aka. a compressed file that contains multiple files), check the 'Unpack Multi-File Archive' check box
  17. Optionally type in a sub-folder into the 'Create in Sub-Folder' text area if you would like to place the uploaded file in a folder other than the 'File' folder
  18. Optionally type in a file description into the 'File Description' text area
  19. Click 'Submit'
  20. Drag your Database into the 'Output Targets' window (if it already doesn't exist within the window)
  21. Drag your uploaded BED file into the 'Input Data' window (if you didn't specify a subfolder when you uploaded it, it will exist within your_group -> Databases -> your_database -> Files -> your_bed_file)
  22. Select the 'Analysis' tab, the 'Track Tools' tab, and 'Coverage Computation'
  23. Customize the coverage tool settings or leave the default
  24. Click 'Submit'
  25. View the output of the read coverage tool by clicking the top menu 'Browser', select your 'Group', select your 'Database', select your 'Entry Point', (optionally select your From and To genomic coordinates) and click 'View'
  26. In order to visualize this track in context of the UCSC browser click on the 'Databases' tab, select your 'Group', select your 'Database', click on '"Big* Files"'
  27. Select 'no file' under the 'BigWig File' column
  28. Click 'Generate Files'
  29. You will receive a message alerting you that your job has been submitted and you will receive an email when this has completed
  30. Click the 'refresh' button to see that your job has been submitted
  31. Click 'refresh' when you receive your response email and you will see that a time stamp has been listed confirming that your job has been completed
  32. Click on the 'Databases' tab
  33. Click on the 'Unlock' tab
  34. Click on 'Generate New Key (Unlock)', which will unlock the database
  35. Click on the 'Databases' tab, select your 'Group', select your 'Database', click on '"Big* Files"', and select your BigWig File (which has the time stamp of your finished job)
  36. Click 'View tracks in UCSC browser'
  37. Finally, select the track you would wish to visualize


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