Remove "Working with the FastQC text output" from episode 02?

[taylorreiter]

Currently, in the "Working with the FastQC text output" of the 02 Assessing Read Quality episode works with the text output of fastqc. This lesson is quite long, and I think most people work with fastqc files only as html output. I know this section is good practice of shell-genomics commands. Could we remove this section, or make it optional? If we remove it, we could make the "Documenting Our Work" section about recording our download & fastqc commands.

Additionally, we could teach multiqc as a replacement to show all of the fastqc files.

Thoughts?

[sstevens2]

AZ bbq : We think it is important to look at the summary files since they may have many files and it is unlikely they will look at the html for all of them. The order may need to be switched where they see and grep a summary file and then download and look at an html file from one that failed.

[taylorreiter]

Could we demo multiqc instead? I have never used the summary files before as I find the visualization to be far for information rich. In my real workflows, I rarely look at individual fastqc files but instead combine them with multiqc.