Hands On Bioinformatics Exercise #2

In [1]:

source bioinf_intro_config.sh
  1. In the More Complex Globs section of the Looping with Globs notebook, we made a glob to refer to MA samples 10 through 19, Lanes 1 through 4. It works, but it is a bit sloppy in places. There are at least two changes that can make the glob more specific, so it is less likely to accidentally match incorrect filenames. Try to figure out those changes:
In [2]:

ls $RAW_FASTQS/1?_MA_*_L00[1-4]_R1_001.fastq.gz

ls: /data/hts2018_pilot/Granek_4837_180427A5/1?_MA_*_L00[1-4]_R1_001.fastq.gz: No such file or directory
  1. In the A globy pipeline section of the Looping with Globs notebook, we used a glob to analyze Lanes 1 through 4 of library 27_MA. Run the trimming and mapping pipeline on Lanes 2 and 3 of library 35_MA.
  2. Now try Running the trimming and mapping pipeline on Lanes 2 and 4 of library 3_MA.

Bonus

  1. Incorporate FASTQC in your analysis pipeline, and run it on Lanes 1, 3, and 4 of 35_MA