The UCSC Repeat Browser contains data first mapped to hg19 or hg38 and then lifted to the consensus sequences (collectively called hg38reps) that make up the Repeat Browser. The datasets mapped include:
| Mapping Alignments | Alignments of each individual repeat instance in hg19 and hg38 back to the Repeat Browser consensus. |
|---|---|
| Mapping Coverage | A coverage plot for the mapping alignments. |
| Conserved Elements | Highly conserved genomic sequences in vertebrates, placental mammals and primates lifted to the Repeat Browser. |
| RepeatMasker Proteins | Protein products of the repeat element as annotated in RepeatMasker records. |
| Other Cons Aln | Alignment of all other Repeat Browser Consensuses against the currently viewed consensus. |
| Repeat Consensus Alignments | Alignment of all repeats from the RepBase RepeatMasker Libraries |
| Tandem Repeats | Detected tandem sequence repeats within the consensus full-length repeat elements. |
| ENCODE Tracks | DNAse mapping, histone marks and TF ChIP-seq from ENCODE lifted to the Repeat Browser. |
| KZNF Tracks (Imbeault/Trono 2017 & Schmittges/Hughes 2016) | Lifting of reprocessed data from large KZNF ChIP-seq screens. |
| TF Differentiation Data (Tsankov 2014) | Lifting of large scale ChIP-seq dataset from differentiation time course across multiple cell types. |
| Stem Cell State Data (Theunissen 2016) | Lifting of reprocessed data from primed and naïve human pluripotent stem cells. |
Complete track descriptions are also available on the browser itself. All datasets can be viewed on the assembly they were mapped to and the Repeat Browser.
Here are some standard files you may need to manipulate the Repeat Browser with other genomic tools:
All Sequences (fasta, one file): hg38reps.fa
2bit file: hg38reps.2bit
“Chromsome” sizes: hg38reps.sizes
liftOver files (from hg38): hg38_to_hg38reps.over.chain
liftOver files (from hg19): hg19_to_hg38reps.over.chain
RepeatMasker annotations (bed files for human genome assemblies)
All other files can be downloaded using the Table Browser feature and selecting the track of interest. Alternatively, you can poke around in these directories and download what you need. Also, check the track descriptions to better understand which file is which.
Source code: Repeat Browser Github