QuickLift Help Page

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 map annotations from hg38 or hg19 to any of the hundreds of new human high-quality genomes in GenArk (HPRC), such as viewing GENCODE genes from hg38 on a T2T assembly like hs1, with almost no additional delay.

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:

1. 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.
2. Open the Convert page by going to View > In Other Genomes (Convert) from the top menu bar.
   
3. 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. 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.
4. 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.

   Note: 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.

   
5. Click Submit. The results page will show the corresponding position(s) in the target assembly with links to the Genome Browser. If any of your visible tracks use a format not supported by QuickLift, the Convert page will display a message: "Some of your tracks failed to lift because the type is not supported by QuickLift." (See Unsupported Track Formats below.)

   If QuickLift was enabled, clicking a result link will display your lifted tracks under a green "QuickLift from ..." group in the target assembly. To remove QuickLift tracks, click the Disconnect button. This removes all QuickLift tracks from the target assembly.

Visual Indicators

QuickLift tracks have a green left-side button bar in the Browser graphic (instead of the usual gray):

An Alignment Differences track also becomes available after running QuickLift, displaying liftOver differences using colored 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 opens a details page showing:

• Source and target assembly genome positions
• DNA sequence alignment
• Type and size of each alignment difference 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