Exercises

SRA Toolkit Exercises

SRA Exercise 1

Find and download RNAseq data from run SRR390925, of experiment SRX112044, publication SRP009873. Copy the file to your home directory on Lonestar at TACC then extract the data in fastq format.

A solution

• SRA search page http://www.ncbi.nlm.nih.gov/sra.
• Type in SRX112044 ? Search
• On experiment summary page click SRR390925
  • takes you to the Run browser where you can see example reads
• Under "Download", "Run" click "ftp" under .sra
  • save the file locally
• Open a Terminal window, change into the directory where the file was stored
• Copy from local machine to TACC

  scp SRR390925.sra username@lonestar.tacc.utexas.edu:~/
  

  • the colon ( after the hostname indicates this is a remote destination
  • the ~/ indicates your home directory

UCSC Genome Browser Exercises

UCSC Exercise 1

Using the UCSC Genome Browser, determine whether Craig Venter or James Watson has a higher risk of Alzheimer's disease.

A Solution

Craig Venter has at least one SNP associated with Alzheimer's disease.

• http://genome.ucsc.edu/ ? Genome Browser ? submit
• type APOE in gene box ? jump
• under "Phenotype and Disease Association" change "GWAS Catalog" from "hide" to "squish" ? refresh
• under "Variation & Repeats" click on "Genome Variants" to see subtrack information
  • note both Venter and Watson have published their genotypes here
  • deselect "1000 Genomes Pilot" tracks (click '-')
  • change "Maximum display mode"  from "hide" to "pack" ? Submit
• zoom in on rs429358. click on rs429358 under "NGRI Catalog... tracks".
  • note association w/Alzheimer's disease
• back in display window, note that Venter has a variant for this SNP while Watson does not

UCSC Exercise 2

Using the UCSC Genome Browser, find and download a list of high-sequencing-depth regions in BED format.

A Solution

• http://genome.ucsc.edu/cgi-bin/hgTable
• clade: Mammal, genome: Human, assembly: hg19
• group: Mapping and Sequencing tracdks, track: Hi Seq Depth
• output format: BED - browser extensible data
• filename: hi_seq_depth.bed
• ? get output
• ? get BED, save to local directory