Table 1 List of Tracks available on the Repeat Browser
Track | Description |
|---|---|
Mapping Alignments | Alignments of each individual repeat instance in hg38 back to the Repeat Browser consensus. |
Mapping Coverage | A coverage plot for the mapping alignments from the above track. |
Annotations (ORFs and UTRs) | Gene annotations of the repeat element as annotated in Dfam or detected by searching the RepeatMasker peptide library. |
Self Alignments | Alignment of all other Repeat Browser Consensuses against the currently viewed consensus. |
GENCODEv32 | Alignments of GENCODEv32 annotated coding sequences, UTRs of protein-coding genes, and ncRNAs to the RepeatBrowser. |
Tandem Repeats | Detected tandem sequence repeats within the consensus full-length repeat elements. |
ENCODE Tracks | DNAse hypersensitive sites, histone marks (UW collection) and TF ChIP-seq (TFBS collection) 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 of TFs involved in differentiation of iPSCs to multiple cell types. |
Stem Cell Naive State Data (Theunissen 2016) | Lifting of H3K9me3 and Kap1 ChIP-SEQ from primed and naïve human pluripotent stem cells. |