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Below are the high-level topics covered in the demonstration.
These topics closely follow the Help documentation.
The demonstration takes place in CGV.


  • Set up an alignment
  • What are we looking at in the viewer?
  • Navigation and zoom
  • Gene search
  • Link to a view of an alignment in GDV, our Genome Data Viewer


Goal: Analyze an expansion within the GPI gene, glucose 6 phosphate isomerase, in T2T-CHM13v2.0. This region was incorrectly collapsed in GRCh38.p14. GPI deficiency is a rare cause of chronic hemolytic anemia.


Here is the workflow exploring the GPI expansion in T2T-CHM13:
  1. Set up an alignment between human T2T-CHM13v2.0 and human GRCh38.p14.
  2. Use "Find a gene in this alignment" to search for glucose 6 phosphate isomerase.
  3. Click on the gene name under "Description". In this case, either assembly will work.
  4. Notice the unaligned region in the long intron in the 3-prime half of GPI.
GPI expansion in T2T


  1. You can analyze the unaligned region by linking to the Genome Data Viewer, GDV. Right-click on either of the alignments to see the pop-up below. I right-clicked on the upstream alignment, the one on the left. Then select, 'View the alignment on T2T-CHM13v.20 in GDV'
Right-click in alignment


In GDV, if necesary, add the track 'T2T/HPRC Assembly-assembly alignments (T2T aligned to h38)' and the track for 'RepeatMasker Repeats.'

This is one possible view in GDV:

That link expires in October, 2023. Here is an image of the view, with an added callout:

Image of GDV showing GPI and unaligned region, plus RepeatMasker


Click here to see the adjustments I made in GDV to get the view above


  • Move the track "NCBI RefSeq Annotation ..." to the top
  • Use the "Region" menu to focus on the GPI gene


GDV Region menu


  • In the track "T2T/HPRC Assembly-assembly alignments, ..." use the gear icon (Track options) to turn off "Project features." This will collapse the transcripts and proteins for a cleaner view.


GDV, turn off Project Features in T2T track

Optional Exercise
Identify a repeat unit present in the expanded, unaligned, region in GPI.


Click here to see how to locate a possible repeat unit


Mouse-over RepeatMasker entries to find a repeat unit


I found more than 400 repeats of GGATCT in the unaligned region of GPI. I downloaded the FASTA for that region to quantify the number of repeats.

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