The UCSC Genome Browser database: 2019 update

Abstract

The UCSC Genome Browser (https://genome.ucsc.edu) is a graphical viewer for exploring genome annotations. For almost two decades, the Browser has provided visualization tools for genetics and molecular biology and continues to add new data and features. This year, we added a new tool that lets users interactively arrange existing graphing tracks into new groups. Other software additions include new formats for chromosome interactions, a ChIP-Seq peak display for track hubs and improved support for HGVS. On the annotation side, we have added gnomAD, TCGA expression, RefSeq Functional elements, GTEx eQTLs, CRISPR Guides, SNPpedia and created a 30-way primate alignment on the human genome. Nine assemblies now have RefSeq-mapped gene models.

Nutrient‐sensitive transcription factors TFEB and TFE 3 couple autophagy and metabolism to the peripheral clock

“…SRR351393 and SRR351397) were downloaded and pre‐processed according to ENCODE pipeline (https://github.com/ENCODE-DCC/chip-seq-pipeline2): Reads were aligned on mouse mm9 reference genome using BWA (Li & Durbin, ), sorted with samtools (Li et al , ), and duplicated reads were removed with MarkDuplicates (http://broadinstitute.github.io/picard/). Peaks were called with MACS (Zhang et al , ; FDR < 0.01) and annotated using CEAS (Ji et al , ) after building custom references using each factor corresponding input as background and current RefSeq genes from UCSC genome browser (Haeussler et al , ). Genes showing a binding site within a distance of 2,000 bp upstream and 1,000 bp downstream the TSS were defined targets, respectively, in mm9 for TFE3 and REV‐ERBα and hg19 for TFEB, for which mouse homologs were determined using NCBI Homologene (Coordinators, ).…”

“…SRR351393 and SRR351397) were downloaded and preprocessed according to ENCODE pipeline (https://github.com/ ENCODE-DCC/chip-seq-pipeline2): Reads were aligned on mouse mm9 reference genome using BWA ), sorted with samtools , and duplicated reads were removed with MarkDuplicates (http://broadinstitute.github.io/picard/). Peaks were called with MACS (Zhang et al, 2008; FDR < 0.01) and annotated using CEAS (Ji et al, 2006) after building custom references using each factor corresponding input as background and current RefSeq genes from UCSC genome browser (Haeussler et al, 2018).…”

Simultaneous discovery of candidate imprinted genes and Imprinting Control Regions in the mouse genome

“…Several publications offer concise overviews about how to use the UCSC browser [38,39]. Default tracks at the browser include the positions of genes, transcripts, the CpG islands, SNPs, and the ENCODE data [37,61]. The positions of SNPs could facilitate designing primers to test the validity of our predictions.…”

“…In exploratory evaluations, we encountered instances where 2 closely spaced peaks produced a robust density peak. ________________________________________________________________________________________ Key features of the genome browser include the option of uploading files to create custom tracks, as shown in this report, and to enhance the resolution of peaks by zooming in to obtain enlarged or close up views [37][38][39]. For example, an enlarged view shows the position of density peaks in a DNA section that covers the subbands in Chr17qA (Fig.…”

MapGL: Inferring evolutionary gain and loss of short genomic sequence features by phylogenetic maximum parsimony

“…MapGL is based on bnMapper (11), which maps genomic sequences across species based on liftover chains (10). We retained the core mapping steps from bnMapper with one modification: while bnMapper drops alignments that are split across chains, we keep the longest alignment among all chains represented.…”