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Overview

Today we are going to hit the ground running to try to make up some ground that we lost yesterday.

Objectives

  1. Complete either the corrected Samtools Tutorial, or the abbreviated cook-book-version. (The cookbook version is worth looking at even if you complete the full tutorial as it teaches another way of executing the same commands)
  2. Go back to the IGV tutorial, look through the E. coli section with particular regard to loading IGV, but don't delay or look too in depth there.
  3. Focus more on the 2nd set of data: Humans.
  4. Copy the human data over to $SCRATCH before the presentation starts to make sure it is available after our break.

 

 

Start File Copy

Since the files will take a while to copy and this can be done in the background, its not a bad idea to start them first. REMEMBER that it is using up 1 of the processors so you are left with 11 to use as you see fit.

Suggested iDEV command and copy command 
idev -m 180 -q normal -A "UT-2015-05-18"
cds
cp -r $BI/ngs_course/human_variation BDIB_Human_tutorial &

Remember we can add the -v option to the cp command if we like some extra peace of mind that files are actually copying and that our terminal hasn't locked up.

 

Set Up IGV

Yesterday we went through how to launch IGV on your local computer (IGV tutorial).

 Review the specifics of IGV in yesterday's tutorial, or click here for a brief summary
Cheatsheet of what to do.
In IGV, use "file -> load from URL" to open each of the following URLs
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12878.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12891.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12892.chrom20.ILLUMINA.bwa.CEU.exome.20111114.bam
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12878.chrom20.GATK.vcf
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12891.chrom20.GATK.vcf
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12892.chrom20.GATK.vcf
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12878.chrom20.samtools.vcf
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12891.chrom20.samtools.vcf
http://web.corral.tacc.utexas.edu/web/GSAF/gva14/NA12892.chrom20.samtools.vcf

 

We will now proceed with the presentation, and hopefully the copy will finish during that.

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