UCSC Genome Bioinformatics

Page Index



This video illustrates how to set up the Genome Browser in the Cloud (GBiC)

run time: 4:16


This video illustrates the features of the gateway page, which provides access to all genome assemblies of the UCSC Genome Browser.

run time: 3:18
 
   
 
 

 
 
 
 

This tutorial shows how to use Multi-Region display mode to substitute alternate haplotypes into the proper place in the genome assembly. For a more comprehensive review of all the features of Multi-Region Display, please see the User Guide.

Transcript of video

0:17 - Set up the Genome Browser display.
0:34 - View alternate sequences.
1:44 - Fetch sequence of right end of alt.
2:55 - Fetch sequence of left end of alt.
3:18 - Blat the alt ends.
4:37 - Substitute alt ends into chromosome.
6:10 - Track lifted from hg19 lacks hg38 annotations on alt.
6:31 - Remove alt from main chromosome.

run time: 7:05


This tutorial demonstrates how to retrieve the coordinates and sequences of exons using the UCSC Genome Browser.

Transcript of video

0:33 - Set up the Genome Browser display.
1:25 - Zoom out to region with several genes.
2:20 - Set up Table Browser.
3:00 - Export exon coordinates.
4:06 - View exons as Custom Track.
5:40 - Export sequences of exons.
7:00 - Confirm that the negative-strand sequences are in the correct sense.
 
run time: 8:12

This tutorial demonstrates the Multi-Region exon-only display mode of the UCSC Genome Browser. For a more comprehensive review of all the features of Multi-Region View, please see the User Guide.

Transcript of video

0:31 - Set up the Genome Browser display.
1:04 - Enable multi-region display: Exon-only.
1:34 - View gene with multiple isoforms.
2:11 - Remove non-coding genes from display.
3:10 - View RNA-seq data in exon-only mode.
 
run time: 5:15  
 
 


This tutorial will demonstrate how to find the tables in the UCSC database that are associated with the data tracks in the Genome Browser graphical viewer.

Transcript of video

0:42 - Set up the Genome Browser display.
1:18 - Turn on data tracks.
2:03 - Find a gene.
2:45 - Find tablename by mouseover.
3:38 - Find tablename by table schema: Use minibutton to access configuration page.
4:33 - Find tablename by table schema: Use track-control link to access configuration page.
4:47 - Find tablename by table schema: Click an individual item.
5:25 - Check contents with Table Browser: All fields.
6:53 - Check contents with Table Browser: Extract selected data fields.
7:25 - Download entire table.
 
run time: 8:39

This tutorial will demonstrate how to locate amino acid numbers for coding genes using the UCSC Genome Browser.

Transcript of video

0:36 - Set up the Genome Browser display.
1:35 - Open genes tracks: UCSC Genes, RefSeq, GENCODE.
2:17 - Locate your gene and zoom to an exon.
3:26 - Turn on RefSeq track coloring-by-codons.
3:51 - Zoom to codon level.
4:23 - Use minibutton for track configuration: Show codon numbering.
5:16 - Configure composite track.
5:44 - Confirm codon numbers with OMIM AV SNPs and UniProt Variants.
7:14 - View UniProt Variants details page.
 
run time: 8:02  
 


This tutorial demonstrates how to find all the single nucleotide polymorphisms in a gene using the UCSC Genome Browser.

Transcript of video

0:43 - Set up Genome Browser display to see your gene.
1:35 - Turn on the SNPs track to see SNPs in your gene.
3:27 - Get SNPs from the Table Browser.
4:36 - Load Table Browser results as a Custom Track.
 
run time: 6:13

This tutorial shows how to find all the single nucleotide polymorphisms upstream from genes using the UCSC Genome Browser.

Transcript of video

0:43 - Set up the Genome Browser display to see your gene.
2:00 - Use the Table Browser to get upstream regions.
3:38 - Paste and view your upstream regions as a Custom Track.
5:23 - Intersect upstream regions with the SNP track.
6:43 - Load upstream SNPs as a new Custom Track.
 
run time: 8:14


This tutorial shows how to use the UCSC Genome Browser to find a list of genes in a given genomic region.

Transcript of video

0:54 - Set up the Genome Browser display to see the genes in your region.
1:31 - Zoom to a cytoband.
1:54 - Display only one isoform per gene.
2:20 - Use the Table Browser to get the list of genes in your region.
3:40 3:40 - Use knownCanonical table in the Table Browser to list only one isoform per gene.
 
run time: 4:33

This tutorial shows how to navigate between exons of a gene using the UCSC Genome Browser.

Transcript of video

1:11 - Zoom to a single exon.
1:55 - Adjust width of graphic display.
2:20 - Highlight a region.
2:39 - Jump to the next exon.
 
run time: 4:25