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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