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UCSC Genome Browser intro
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The UCSC Genome Browser is an invaluable resource both for obtaining public sequencing data and for visualizing it.
Demo - Data resources
- http://genome.ucsc.edu/ Genome Browser, submit
- navigaion
- type GAPDH in gene box, jump
- note zoom out/zoom in buttons; click on position or click/drag
- track detail
- click "Multiz Alignments" to expand track detail
- click on one of the SNP to expand track detail
- then click on the snp name to see details
- selecting tracks
- under "Regulation" section, change Regulation track from "show" to "hide", refresh
- right click "Multiz Alignments", hide
- under "Phenotype and Disease Association" change GWAS Catalog from "hide" to "squish", refresh
- type PRNP in gene box, jump.
- click on "NHGRI Catalog..." track description to expand detail
- note correspondence between SNPs (SNP 132) and disease SNPs (GWAS)
- click on one of the disease SNPs for detail
Exercise 1
Using the UCSC Genome Browser, determine whether Craig Venter or James Watson has a higher risk of Altzheimer's disease.
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APOE gene.
Variation & Repeats, Genome Variants
Phenotype & Disease Assocations, GWAS Catalog
Demo - Downloading annotation data
For RNAseq you often need a GTF file, but how do you find them? One way is to download annotations from the UCSC Table browser in GTF format:
- http://genome.ucsc.edu/cgi-bin/hgTables
- clade: Mammal, genome: Human, assembly: hg19
- group: Genes and Gene Prediction tracks, track: RefSeq genes
- output format: GTF - gene transfer format
- optional: enter filename in typein box
- get output
Exercise 1
Using the UCSC Genome Browser, find and download a list of high-sequencing-depth regions in BED format.
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group: Mapping and Sequencing tracdks
track: Hi Seq Depth