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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