Next week, NCBI staff will attend AGBT in Marco Island, Florida. On Tuesday, February 25, 2020, three posters from NCBI staff will be on display from 4:40 p.m. – 6:10 p.m. during the Poster Session and Wine Reception in the Banyan and Calusa Ballroom Foyers, Levels 1 and 3. Read on to learn a little bit about what we’ll be presenting.
Tag: Sequence Viewer
Have you ever wanted a list of the genes you’re looking at in the browser – maybe to give you a starting point for candidate gene analysis, or to cross-reference with other data?
In response to your feedback and helpful discussions with you, we’re excited to announce a new option to download gene annotation data directly from the web sequence viewers and browsers.
This new feature lets you get a table of gene names, coordinates and other helpful information from your genomic region of interest.
Go to the Download menu on the toolbar of the graphical viewer to find options for getting sequence and annotation data.
Check out the latest videos on YouTube to learn how to best use NCBI graphical viewers, SRA, PGAP, and other resources.
Genome Data Viewer: Analyzing Remote BAM Alignment Files and Other Tips
This video shows you how to upload remote BAM files, and succinctly demonstrates handy viewer settings, such as Pileup display options, and highlights the very helpful tooltips in the Genome Data Viewer (GDV). There’s also a brief blog post on the same topic.
NCBI’s genome browsers and graphical sequence viewers now allow you to view BAM alignments sorted by haplotype tag. This option is useful for analyzing variants within a sequenced sample and can help you detect or validate structural variants.Figure 1. Remote BAM alignment data sorted by haplotype tag in the Genome Data Viewer. The remote BAM file was added through the “User Data and Track Hubs” feature in GDV. You can load the remote BAM for this example through https://go.usa.gov/xpM9c. The sorted display shows that haplotype 1 contains a significant deletion in this region relative to haplotype 2 and the reference genome assembly. Aligned reads not assigned a haplotype tag in the BAM file are grouped under the heading “haplotype not set” (not shown).
You now have access to bulk settings options for track hubs in the Genome Data Viewer (GDV) and Sequence Viewer. These settings allow you to pick the default tracks that load into the viewer from your chosen track hub. You can access the bulk options menu for by clicking on the collapsed menu or “hamburger” icon (stack of horizontal bars) at the right end of the track grouping in the Configure Track Hubs dialog (Figure 1).Figure 1. The Configure Track Hubs dialog in GDV. You can activate the bulk settings menu for a connected track hub by clicking on hamburger icon at the right of the track grouping. Clicking Select Default tracks checks on all of the tracks in that grouping, Smoothed PhyloCSF in this case. Continue reading “Bulk track hub settings now in Genome Data Viewer”
You can now download images in both PDF and Scaled Vector Graphics (SVG) formats from our Sequence Viewer and genome browsers such as the Genome Data Viewer! SVG files are ideal for editing in image editors and provide high quality graphics for publications, posters, and presentations. Both the PDF and SVG files that you download contain vector graphics for high fidelity images.
You can download image files by choosing the “Printer-Friendly PDF/SVG” option under the Tools menu from any Graphical Sequence Viewer application (Figure 1).
Figure 1. Printer friendly download options from the graphical view in the Genome Data Viewer. You can download either PDF or SVG formats, which are easily edited in standard graphics applications.
You can now access NCBI’s Genome Data Viewer directly from the Track Hub Registry at EBI!
When you search for a track hub in the Track Hubs Registry, you now have the option to open the hub with NCBI GDV.
On June 18, 2019, NCBI’s Sanjida Rangwala will demonstrate the rich data visualization capabilities of NCBI’s genome browser at a conference that is part of the Rocky Mountain Genomics Hackcon. As mentioned in a previous post, NCBI staff will also participate in an NCBI-style Hackathon as part of the larger event. The genome browser presentation and demonstration will show you how to create visuals that provide insights and show connections among genes, transcripts, variation, epigenomics and GWAS data from NCBI sources. You will also see how you can upload your own data and embed NCBI viewers on your own pages.
Earlier this year, NCBI announced plans to retire the Clone DB web interface. Pursuant to this retirement, starting on May 27, 2019, all web pages associated with Clone DB and CloneFinder will redirect to this blog post. Links to Clone DB from the NCBI home page will also be going away.
Did you know you can easily switch between gene feature modes in NCBI’s graphical sequence displays like Sequence Viewer and GDV? You may need to configure gene tracks to suit your needs if, for example, you need to conduct analyses or present quality images.
Use one of two easy access points to the gene configuration menu to show the gene bar, the single line gene model or the expanded modes that show transcripts and CDSs.