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This tutorial shows how to use the UCSC Genome Browser to find a list of genes in a
given genomic region.
Transcript of video
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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
- Use knownCanonical table in the Table Browser to list only one isoform per gene.
run time: 4:33
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This tutorial shows how to navigate between exons of a gene using the UCSC Genome Browser.
Transcript of video
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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
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This tutorial demonstrates how to find all the single nucleotide polymorphisms
in a gene using the UCSC Genome Browser.
Transcript of video
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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
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This tutorial shows how to find all the single nucleotide polymorphisms
upstream from genes using the UCSC Genome Browser.
Transcript of video
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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
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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
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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
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This tutorial will demonstrate how to locate amino acid numbers for coding
genes using the UCSC Genome Browser.
Transcript of video
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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
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This tutorial demonstrates how to retrieve the coordinates and sequences of exons using
the UCSC Genome Browser.
Transcript of video
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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
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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
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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
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This video illustrates the features of the gateway page, which provides access to
all genome assemblies of the UCSC Genome Browser.
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run time: 3:18
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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
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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
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