Independent Exercise - SBATCH, Conda, Filtering our BAMs

Filtering All Samples

15 Minutes

We just learned how to activate an existing conda environment and use it to provide software that we want - samtools - and use samtools to filter our BAM files. We also recently learned how to create SBATCH script files and submit them using sbatch.

Let’s combine these ideas and filter the rest of our BAM files.

If you have extra time, there’s a bonus exercise of indexing your BAMs as well

Instructions:

• Work independently in the main room, posting any questions that arise to slack.
• Recommendations for writing your own code:
  • Read function documentation
  • Test out ideas - it’s okay to make mistakes and generate errors
  • Use a search engine to look up errors or recommended solutions using keywords
• We’ll review possible solutions after time is up as a group.

• Review our samtools command that we used earlier. Combine this with what we’ve learned about using conda environments and creating SBATCH files.
• Create an SBATCH file that activates our samtools_deeptools conda environment. With the conda environment active, use samtools to filter sample_A.
• Submit the SBATCH file, view the output, and verify once it’s complete that we have created the filtered sample_A BAM file.
• Once we are happy with the results, create additional SBATCH files for our other samples, and submit them as well.

Bonus: If you have extra time, extend this exercise and use samtools index to index the filtered BAM file for sample_A.