64f5e1fb8b93253cf89a6f36fb00d67d2ededf1d
gperez2
Sun Mar 15 20:52:02 2026 -0700
Updating the QuickLift documentation page and the Alignment Differences page, refs #35536
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+
+
+
+
+
Overview
+
+An alignment between two DNA sequences maps every nucleotide in one sequence to a nucleotide in
+another sequence. By making and using
+whole-genome alignments,
+the UCSC Genome Browser always allowed users to "lift" genome annotations to another
+assembly (liftOver), in bulk, one track at a
+time. QuickLift is a tool that uses the same algorithm, but it maps
+(liftOver) annotations on demand, in real-time, for all visible tracks. Only the
+annotations in the currently visible region are lifted, so this is usually fast enough when
+browsing a genome. For example, QuickLift can be used to map
+annotations from hg38 or hg19 to any of the hundreds of new human high-quality genomes in GenArk
+(HPRC), with almost no additional delay. For instance, you can view GENCODE genes from hg38
+on a T2T assembly like hs1, carrying over your visible tracks to the target genome assembly.
+
+
+QuickLift functionality depends on the availability of alignment files
+(chains) that describe how sequences in one assembly correspond to another. The alignment files are
+currently made at UCSC, and if no alignment file is available for the assembly in which you're
+interested, please send a request to the genome mailing list, and we will attempt to provide you with one.
+
+
+
+
Getting Started
+
+The source assembly is the assembly where the annotations come from, and the
+destination (target) assembly is the assembly you are converting to.
+To use QuickLift, follow these steps:
+
+
+
Navigate to the genome assembly and position you want to convert in the
+ Genome Browser. Make sure the
+ tracks you want to lift are visible.
+
Open the Convert page by going to View > In Other Genomes (Convert)
+ from the top menu bar, or navigate directly to
+ the Convert page.
+
Under Destination, choose the target genome assembly. You can either:
+
+
Use the Search bar to find a target genome by name. As you type,
+ an autocomplete dropdown appears with matching genomes. The search
+ automatically filters results to show only assemblies that have a liftOver
+ chain available from your source assembly. Genomes without an available
+ liftOver chain are excluded from the results. You can also click the
+ dropdown toggle button to browse recent and popular genomes.
+
Use the Assembly dropdown to select from other assemblies
+ of the same organism (e.g., other human assemblies when the source assembly is
+ hg38). To convert to a different organism, use the Search bar
+ instead.
+
+
+
Check the QuickLift tracks checkbox to carry over your visible tracks,
+ custom tracks, and track hubs to the target assembly. Without this checkbox, only the
+ coordinate position is converted.
+
+
When a single track from a container track, such as a superTrack or
+ composite, is lifted, the entire container track is carried over to the
+ target genome assembly.
+
+
+
+
+
+
Click Submit. The results page will show the corresponding position(s)
+ in the target assembly with links to the Genome Browser. If
+ QuickLift was enabled, clicking a link will display your
+ lifted tracks under a green
+ "QuickLift from ..." group in the target
+ assembly. To remove QuickLift tracks, click the
+ button.
+
+
+
+
Visual Indicators
+
+QuickLift tracks have a green left-side button bar in the Browser
+graphic (instead of the usual gray):
+
+
+
+
+
+The Alignment Differences track displays liftOver differences using triangles and lines:
+
+
+
Insertions: green
+
Deletions: blue
+
Double-sided insertions: gray (Both the source
+ and target assemblies contain unalignable sequence between two regions of aligned
+ sequence)
+
Mismatches: red
+
+
+Mousing over a triangle displays the size base-pair (bp) difference and the type of alignment
+difference.
+
+
+
+
+
+Clicking a triangle provides the source and target assembly genome positions, DNA sequence
+alignment, including the type of alignment difference with the bases within the currently
+visible browser region.
+
+
+
Unsupported Track Formats
+
QuickLift does not support the following track formats:
+
+
WIG — bigWig
+ is supported; WIG tracks can be converted to bigWig using the
+ wigToBigWig
+ utility
+
BAM
+
CRAM
+
PSL — BED
+ is supported; PSL tracks can be converted to BED using the
+ pslToBed
+ utility
+
VCF
+
HIC
+
MAF
+
bigChain
+
Interact
+
narrowPeak / broadPeak —
+ bigBed
+ is supported; since narrowPeak and broadPeak are BED-based formats, they can be
+ converted to bigBed using the
+ bedToBigBed
+ utility
+
pgSnp
+
+
+
+
Resources & Support
+
+
LiftOver — convert
+ coordinates or annotation files in bulk between assemblies
+
Chain format —
+ description of the alignment chain files used by
+ QuickLift and liftOver
+
Contact us — request a new
+ liftOver chain or report issues via the genome mailing list
+ 
+
+