Day 1 Take Away Points

TACC

• Submitting a job on TACC=  Sending  a series of commands to be run on the >1000 compute nodes.
• Put all your commands in a commands file (call it whatever you'd like)
• Create a launcher.slurm file which provides queue, allocation, time etc and points to the commands file you created. 
• Submit the job by submitting the launcher.slurm file.

When designing your RNA seq experiment

• When creating RNA-Seq libraries, you have lots of options: strand specific vs non strand specific, ribosomal depletion etc.
• Decisions depend on your questions. 
• For differential expression studies, number of replicates is most important. For assembly and annotation of transcriptomes or for identifying rare/novel transcripts, depth of coverage becomes important.

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 for doing these operations.
• Now it's ready for mapping.
  
  

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