Day 1 Morning - Githubissues

[x] - Providing Unix exercise data to Zena to use for Data Carpentry.
[x] - Move Fastq QC and Trimming to Day 1 Afternoon.
[x] - Mention SLURM and how to implemet it instead of PBS script. [Zena]
[x] - Add a more detailed For loop explanation to set people up for a for loop exercise
[x] - Put fasta_counter example in shell script
[x] - Change fasta_counter to run for loop on all files in directory
[x] - show them how to pair fastq samples in shell script using unix commands documentation pending
[x] - script to pair fastq samples in shell script
[x] - Use a simple AWK command for fastq data statistics. Give a more clear explanation for AWK command structure.
[x] - Simplify awk commands for fastq statistics
[ ] - gff_counter shell script => goes through each gff file in a directory and prints the number of CDS genes
[ ] - Add simple unix commands to explore fastq files
[x] - Move R to the end and
[x] - potentially add some additional plotting examples?
[x] - Make sure before the workshop that you have moved the day1_morn data files to day1_after.
[x] - Ask Zena about the collistin resistant example dataset for variant calling.

alipirani88 / Comparative_Genomics