Liftoff uses Minimap2 to align reference gene DNA sequences to the target genome and selects the alignment(s) concordant with the intron/exon structure with the highest sequence identity. A minimum sequence identity of 95% was required to annotate gene paralogs. After running Liftoff, we identified genes that did not overlap any CAT annotations using bedtools intersect. These were combined with the CAT annotation to create the final annotation.
++The raw data can be explored interactively with the +Table Browser or the +Data Integrator. The data can also be +accessed from scripts through our REST +API, where the track name is catLiftOffGenesV1.
++For automated analysis, the data may be downloaded from our +download +server as a bigGenePred file. The file for this track is called +catLiftOffGenesV1.bb. Individual regions or the whole genome annotation can be obtained +using our tool bigBedToBed, which can be compiled from the source code or downloaded as a +precompiled binary for your system. Instructions for downloading source code and binaries can be +found here. The tool can also be used to obtain only features within a given range, +for example:
+bigBedToBed https://hgdownload.soe.ucsc.edu/gbdb/$db/catLiftOffGenesV1/catLiftOffGenesV1.bb -chrom=chr6 -start=0 -end=1000000 stdout ++Please refer to our +mailing +list archives for questions, or our +Data Access FAQ for more +information.
+This track was provide by Marina Haukness <mhauknes@ucsc.edu> of UC Santa Cruz and Alaina Shumate <ashumat2@jhmi.edu> of Johns Hopkins University.
Fiddes IT, Armstrong J, Diekhans M, Nachtweide S, Kronenberg ZN, Underwood JG, Gordon D, Earl D, Keane T, Eichler EE et al. Comparative Annotation Toolkit (CAT)-simultaneous clade and personal genome annotation. Genome Res. 2018 Jul;28(7):1029-1038. PMID: 29884752; PMC: