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BME 383J Course Content

Created by Scott Patrick Hunicke-Smith, last modified on Nov 13, 2012

BME 383J Course Content

Your Instructors

Name	Initials	Affiliation	Expertise
Scott Hunicke-Smith	SPHS	Director GSAF	Everything, if loosely defined (but especially `awk`)
John Fonner	JF	Research Associate, TACC Life Sciences	high performance computing
Matt Vaughn	MWV	Manager, TACC Life Sciences	in absentia
Jeff Barrick		Asst. Prof. Biochemistry	in absentia

Tuesday Nov. 6th

Introduction to next-gen sequencing technologies (SPHS - 15 minutes)
- Official Illumina video | Another Illumina video
Intro to TACC/Linux (JF - 15 minutes)
- About TACC
- Getting Started at TACC
- If you are new to Linux, there are some basics here, and some tips, techniques, and practice exercises here.
Introduction to mapping presentation (SHS - 45 minutes)
- Side content: what's this all about? Check out this short wiki page on genome variants

Homework - expand this section for the assignment

Log in to Lonestar via ssh
Copy data files that will be required for Thursday's homework:
1. Define a BASH variable to the genomics data repository at TACC like this:
  How to define the variable BI in a bash shell
```
BI="/corral-repl/utexas/BioITeam"
```

Find $BI/ngs_course/intro_to_mapping/data
Copy the three data files you find there to your scratch directory (see the Lonestar user's guide if you need help to get to your scratch directory).
Figure out how to load the modules for samtools and bwa. Lonestar user guide helps here too.
Bonus #1 - extract the genome from the gbk file and then map the fastq files to that genome. Help can be found elsewhere on this wiki site.
Bonus #2 - do the human data scavenger hunt at the bottom of this wiki page (can be done on any computer - doesn't need TACC) to see what NGS data looks like.

Thursday Nov. 8th

Mapping & Variant calling
- Mapping theory (SPHS)
  - http://last.cbrc.jp/mcf-kyoto08.pdf
  - http//www.cs.utsa.edu%2F~jruan%2Fteaching%2FCS6293_fall_2010%2Fslides%2Fslide5_shortreadmapping.ppt
- Mapping & variant calling practice - haploid (bacteria) (JF)
- Variant calling (homework)

Homework - expand this section for the assignment

Go to this web page and call variants from real human genomes from the 1000 genomes project.
Helpful hint: start this early - it involves some long run times at TACC.
IMPORTANT NOTE: you must use "-a BME2012" with the launcher_creator.py command.

Tuesday Nov. 13th

Review NGS - from cellular DNA to variant data
Review results of variant calling - for these examples, Start IGV, load the genome, "Human (1kg, b37+)", load the three NA*.bam files (the corresponding *.bai must exist in the same directory).
Command to view the contents of a sorted (by genome coordinates) BAM file
```
samtools view NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | head
```
Examine the first read of the file which matches at genome position chr20:59993
- Examine a pileup in text and in IGV
  Command to generate a "pileup" - data oriented in "genome coordinates" by genome base-pair
```
samtools mpileup -f ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | more
```
  Examine the area around chr20:60614
- Examine a variant in text and in IGV
  Command to call variants
```
samtools mpileup -uf ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools view -vcg - | more
```
  - look at the SNP at base 76771
  Examine the SNP at chr20:76771
SNP Annotation
Reference databases (if time permits)

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