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.
BACK TO COURSE OUTLINE
