IGB Release Documentation
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  1. Open the H_sapiens_Dec_2013 genome
  2. Add a Data Source using the following URL (if not already added): https://quickload-testing.s3.amazonaws.com/smokeTestingQuickload/
  3. Navigate to chr2:232,546,991-232,551,587
  4. Check that only the RefSeq Curated annotation is loaded
  5. Right-click on the track name and select Filter...
    1. In the Add/Remove/Edit Filters window, click Add
      1. In the Add filter window, use the dropdown to select Reads with no gaps
      2. Click OK
    2. Click OK

  • Check that the track matches the image above.
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  1. Right-click on the track name and select Filter...
    1. In the Add/Remove/Edit Filters window, select Reads with no gaps
    2. Click Remove
    3. Click OK
  • Check that the filter is removed and the missing annotations are visible.
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  1. Navigate to chr16:28,931,601-28,939,711
  2. Add the Bam - CD19 Single-cell RNA-Seq from 10X Genomics file to IGB
  3. Click Load Data
  4. Right-click on the track name and select Optimize Stack Height
  5. Right-click on the track name and select Filter...
    1. Click Add
      1. Select SAMtags
      2. Select CB
      3. In the value field, enter the following: GGTGAAGAGGGAGGAC-1;GGGACCTGTATCGTAC-1;AAGACTCTCGAGTTGT-1;TTAGTCTAGACAACAT-1;ATACCGAGTTCGTAAC-1
      4. Click OK
    2. Click OK

  • Check that the track matches the image above.
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  1. Right-click on the track name and select Filter...
    1. Click Edit
      1. Select =/= (does not equal) from the comparator drop-down menu
      2. Click OK
    2. Click OK

  • Check that the track matches the image above.
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  • The filter settings were the same after closing and opening the Edit filter window.
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  1. Install the Monster Alignment Filter plugin through the IGB App Manager (Tools > Open App Manager)
  2. Right-click on the track name and select Filter...
    1. Click Add
      1. Select Reads without monster gaps
      2. Set the Max intron size to 4000
      3. Click OK
    2. Click OK

  • Check that the track matches the image above.
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Color by...

  1. Right-click on the track name and select Color by...
    1. In the Color By window, use the dropdown to select SAMtags
    2. Click Configure Tag Color Mapping
      1. Add the following Tag Values:
        1. 60M30S
        2. 90M
        3. 30S60M
      2. Assign each row a unique color
      3. Check the box next to each row you added a Tag Value to
      4. Click Save and Apply
      5. In the SAMtag field, type CIGAR
      6. Click Save and Apply
    3. Click OK

  • A warning appeared when Save and Apply was clicked before setting a SAMtag value.
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  • The track matches the image above.
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  1. Right-click on the track name and select Color by...
    1. Click Configure Tag Color Mapping

  • The table still contains the tags and colors you input previously.
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Click Clear all

  • The Color by table is now empty.
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  1. Download this CSV file from Google Drive: https://drive.google.com/file/d/1lwrytvVVnjscgp5LeHNm6NEGu4M0pwgd/view?usp=drive_link
  2. Click Import...
    1. Select the CSV file you just downloaded (10k_PBMC_3p_nextgem_Chromium_X_cloupe_withColors.csv)
  3. From the SAMtag drop-down menu, select CB
  4. Click Save and Apply

  • The track matches the image above.
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  1. Right-click on the track name and select Color by...
  2. Click Configure Tag Color Mapping
  • The Color By window appeared immediately.
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  1. Download this second CSV file from Google Drive: https://drive.google.com/file/d/1BabbrioCR_k4IW9rUX6zhvZ1VhA3vwMw/view?usp=drive_link
  2. Click Import...
    1. Select the CSV file you just downloaded (10k_PBMC_3p_nextgem_Chromium_X_cloupe.csv)
  3. Click View by Cluster
  4. Assign a unique color to each cluster
  5. Select CB
  6. Click Save and Apply

  • The track looks similar to the image above.
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  • No errors in the Log.
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  1. Open the A_thaliana_Jun_2009 genome
  2. Navigate to Chr1:6,709,263-6,716,866
  3. Check that the Araport annotation is loaded
  4. Right-click on the Araport track name and select Color by...
    1. In the Color By window, use the dropdown to select Length
    2. Click on the Edit button next to heatmap
      1. In the Configure Heatmap window, click on Set Range
        1. In the Set Range window, set the Min to 200 and the Max to 2000
        2. Click OK
      2. Double-click the right-most arrow
        1. In the Select new color window, select red
        2. Click OK
      3. Double-click the arrow to the left of the right-most arrow
        1. In the Select new color window, select another shade of red
        2. Click OK
      4. Click OK
    3. Click OK

  • Check that the track matches the image above.
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  1. Right-click on the Araport track name and select Color by...
    1. In the Color By window, use the dropdown to select None.
    2. Click OK
  • Check that the track color is reset back to its original color (should be black).
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