+ -This track shows mismatches between the assembly from which the track was quickLifted and the current genome. +The Alignment Differences track shows mismatches and indels between the assembly from which the +track was QuickLifted and the current genome. +
+ ++Visible tracks, custom tracks, and track hubs on the Browser graphic page are carried over (lifted) +to the new assembly using the QuickLift tracks checkbox. 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 new assembly. +
+QuickLift tracks appear under a green +"QuickLift from ..." group in the New assembly. +QuickLift tracks can be removed by the + button. 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; mousing over a triangle displays base-pair (bp) information. Lines and triangles are +color-coded as follows: +
+
+ Clicking a triangle provides additional information about the alignment.
+ ++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 (Kent et al., 2003), +genome annotations can be "lifted" 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. +
+ ++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, but we are working on making the pipeline to align two genomes more widely +available. +
+ ++Kent WJ, Baertsch R, Hinrichs A, Miller W, Haussler D. + +Evolution's cauldron: duplication, deletion, and rearrangement in the mouse and human +genomes. +Proc Natl Acad Sci U S A. 2003 Sep 30;100(20):11484-9. +PMID: 14500911; PMC: PMC208784 +