1. Alignment re-cap
- Remember those three checks after read alignment:
- BAM file?
- Sorted?
- Indexed?
- Explain the difference between alignment score and mapping quality in SAM/BAM files including which fields they are being stored in.
- Run
bamqc on your BAM files (Note: this is a tool that’s not available in spack, but you can use it via /softlib/apps/EL7/BamQC/bin/bamqc after logging in to farina or buddy). You will need to figure out how to run this on your own (hint: /softlib/apps/EL7/BamQC/bin/bamqc --help).
- Describe 3 differences between the
bamqc results for both the BWA and the STAR output files.
- Find a read that has been aligned with a split in
STAR. How did BWA handle the mapping of that read?
- How can you remove the unmapped reads from the
BWA output? (hint: go back to the notes where FLAG values were explained)
2. Get git talking to RStudio.
Make use of Akanksha’s office hours!!
- Work through the git tutorial at https://happygitwithr.com/. At a bare minimum, get Rstudio talking to git on your local machine; try to get RStudio talking to GitHub, i.e. chapters 6-13.
Project work: (due on Feb 18!)
If you need a different program than what we have used in the class, you can use spack find to see if the tool is already installed and loadable via spack. If your tool is not there, get in touch with scu@med.cornell.edu to ask them to install it for you.
If you have processes that will take a long time, go back to the notes from the first day and try to make use of sbatch.
- Download at least one FASTQ file that you will be working with for your project. Document the following details:
- where did you get it from?
- what publication is it linked to?
- who generated the data?
- how was the NA extracted?
- what library prep was used?
- what cell type was used?
- what was the treatment/experimental condition?
- what sequencing platform was used?
- Align the FASTQ file with an appropriate aligner (you may have to build a new index). Document:
- parameters (and why you chose them)
- summary of outcome and basic QC
Compile the .Rmd file and send both the .Rmd and the HTML files to angsd_2019@zoho.com by Monday night.