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.

 

Step 1: idev

First things first, start an idev node on the normal queue and request it for ~180-200 minutes to cover the entire length of the class. 

idev -m 180 -q normal -A "UT-2015-05-18"

 

Step 2: Start File Copy

Since the files can 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.

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, but that isn't as useful when running in the background.

 

Step 3: Finish Samtools tutorial

Either method is fine, but you should look at the abbreviated version as it introduces a new type of command execution:

  1. Full tutorial
  2. Abbreviated tutorial

Step 4: IGV

Go through the IGV tutorial paying special attention to how to load IGV on your local computer and the  2nd set of data covering human information.





 

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

Cheatsheet of what to do.
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.