I believe it is a little abrupt to go from "this is grep" to assessing read quality using grep. I wonder if an example just using the general nucleotides would help the students grasp grep a little better before jumping right into unknown nucleotides. Such as adding in:
grep ATGC SRR098026.fastq
just to print out all of the instances of ATGC. Then explaining that there are instances of N and N can mean aNy nucleotide and then using grep to search for NNNNNNNNNN as a way to check quality.
I believe it is a little abrupt to go from "this is grep" to assessing read quality using grep. I wonder if an example just using the general nucleotides would help the students grasp grep a little better before jumping right into unknown nucleotides. Such as adding in:
grep ATGC SRR098026.fastq
just to print out all of the instances of ATGC. Then explaining that there are instances of N and N can mean aNy nucleotide and then using grep to search for NNNNNNNNNN as a way to check quality.