SRA Toolkit Exercises
SRA Exercise 1
Find and download RNAseq data from run SRR390925, of experiment SRX112044, publication SRP009873. Copy the file to your Scratch area on Stampede2 at TACC then extract the data in FASTQ format.
A solution
- SRA search page http://www.ncbi.nlm.nih.gov/sra.
- Type in SRX112044 then Search
- On experiment summary page click SRR390925
- takes you to the Run browser where you can see example reads
- Under "Download" tab, select Reads
- This tells you that you need the SRA Toolkit to fetch the Run data
Login to stampede2:
ssh username@stampede2.tacc.utexas.edu:~/
check that the file is in your Scratch area
Once on stampede2 (prompt: stamp2$)cds ls SRR390925.sra
if not, copy it from our course area:
Once on stampede2 (prompt: stamp2$)
Find the SRA toolkit module
module load biocontainers module spider sratoolkit ------------------------------------------------------------------------------------------------------ sratoolkit: sratoolkit/2.8.2 ------------------------------------------------------------------------------------------------------ Description: The SRA Toolkit and SDK from NCBI is a collection of tools and libraries for using data in the INSDC Sequence Read Archives This module can be loaded directly: module load sratoolkit/2.8.2 Help: The sratoolkit module file defines the following environment variables: - TACC_SRATOOLK_DIR - TACC_SRATOOLK_EXAMPLE - example files To improve download speed, the prefetch command has been aliased to always use aspera. We also suggest running $ scratch_cache to change your cache directory to use the scratch filesystem. Documentation can be found online at https://github.com/ncbi/sra-tools/wiki Version 2.8.2
Load the module
module load sratoolkit
Invoke fastq-dump with no arguments to see basic usage information.
Usage: fastq-dump [options] <path> [<path>...] fastq-dump [options] <accession> Use option --help for more information fastq-dump : 2.8.2
Extract to FASTQ
fastq-dump SRR390925.sra # Output should look like this: Written 1981132 spots for SRR390925.sra Written 1981132 spots total
Look at some data
ls SRR390925.fastq SRR390925.sra head SRR390925.fastq @SRR390925.1 ROCKFORD:1:1:0:1260 length=36 NCAACAAGTTTCTTTGGTTATTAACTACGACTTACC \+SRR390925.1 ROCKFORD:1:1:0:1260 length=36 \#CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC @SRR390925.2 ROCKFORD:1:1:0:293 length=36 NAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAAA \+SRR390925.2 ROCKFORD:1:1:0:293 length=36 \#################################### @SRR390925.3 ROCKFORD:1:1:0:330 length=36 NAAAAAAAAAAAAAAAAAAAAAAAATAAAAAAAAAA
Count lines and number of reads (fastq has 4 lines/read)
login2$ wc -l SRR390925.fastq 7924528 SRR390925.fastq login2$ echo $((7924528 / 4)) 1981132
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