Day 1 Take Away Points 2014

TACC

  • Submitting a job on TACC=  Sending  a series of commands to be run on the 1888 compute nodes.
  • Put all your commands in a commands file (call it whatever you'd like)
  • Create a launcher.sge file which provides queue, allocation, time etc and points to the commands file you created. 
  • Submit the job by submitting the launcher.sge file.


When designing your RNA seq experiment

  • When creating RNA-Seq libraries, you have lots of options: strand specific vs non strand specific


Once you get your RNA-Seq data

  • Check for low quality bases, low quality reads, overrepresented sequences, and sequence duplication using fastqc.
  • If needed, trim low quality bases, filter low quality reads, trim adaptors.  We covered fastx_toolkit and cutadapt for doing these operations.

For mapping your reads to reference

  • Unspliced mapper- BWA: We ran BWA mem algorithm to map simulated rna seq data to the genome.
  • After mapping, samtools to get some statistics from mapping results. We'll be going back to this again!
 

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