BME 383J Course Content
Your Instructors
Name | Initials | Affiliation | Expertise |
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SPHS | Director GSAF | Everything, if loosely defined (but especially | |
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)
- 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
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- 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)
- Mapping theory (SPHS)
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Go to this web page and call variants from real human genomes from the 1000 genomes project. |
Tuesday Nov. 13th
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- 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).
Examine the first read of the file which matches at genome position chr20:59993Code Block title 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 a pileup in text and in IGV
Examine the area around chr20:60614Code Block title 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 a variant in text and in IGV
- look at the SNP at base 76771Code Block title Command to call variants samtools mpileup -uf ref/hs37d5.fa NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam | bcftools view -vcg - | more
Examine the SNP at chr20:76771
- Examine a pileup in text and in IGV
- SNP Annotation
- Reference databases (if time permits)