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.