change quality encoding scale in 02 Assessing Read Quality

[taylorreiter]

In 02 Assessing Read Quality, quality encoding only goes up to 40, but J = 41, and K = 42. This is confusing because the read we use as an example has Js in it. We should change the example from:

Quality encoding: !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHI
                  |         |         |         |         |
Quality score:    0........10........20........30........40 

Quality encoding: !"#$%&'()*+,-./0123456789:;<=>?@ABCDEFGHIJK
                  |         |         |         |         |
Quality score:    0........10........20........30........40.. 

[taylorreiter]

This would be solved by #127.

[ErinBecker]

#127 has merge conflicts. Any volunteers to fix that up? 😄

[fpsom]

I'm not really sure that #127 is still applicable. In the updated version, there is a short description of the FASTQ format (Section "Details on the FASTQ format" in the 2nd episode), which could be removed if already present in the shell genomics one. However, I would argue (for completeness purposes) that we maintain that part in - maybe put it under a different color? @aschuerch @taylorreiter thoughts?

[taylorreiter]

@fpsom these lessons are already quite long. I would vote to link to the shell genomics lesson that covers this material, which was updated with here. Does this sound ok? If so, I will address merge conflicts with #127

[fpsom]

@taylorreiter I definitely won't argue about the length. However, I'd be much happier if, after removing the entire section, we insert a sentence and a direct link to the shell genomics section, so that the learners can easily connect there for reference. Sounds reasonable?

[taylorreiter]

That sounds like a great plan! I will put in a PR to address this by the end of the week. Because #127 has merge conflicts given that it was suggested prior to the lesson update, I will put in a new PR that is in the same spirit as #127 if that's ok with you @fpsom!

[aschuerch]

At this moment it is present in both Shell and Wrangling, however the example in Shell (with a lot of NNNs) makes it hard to explain the phred scores

[sstevens2]

AZ bbq: We agree that this quality score section should only be shown once.

[murraycadzow]

One of our learners spotted this during our workshop too and it caused confusion why the score shown ends at "I" but the example read immediately below contains "J"