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!