Be careful describing Kallisto and Salmon

[tbooth]

From @cmeesters:

Kallisto performs (wording according to docs) a "pseuoalignment" - it is not a classical aligner and should
not be mentioned as such.

"If you know about the Kallisto software..." make no such assumption. Explain, not presume presumptuous.

[tbooth]

Kallisto performs (wording according to docs) a "pseuoalignment" - it is not a classical aligner and
should not be mentioned as such.

Very true. This was lazy on my part. I've corrected the descriptions of both Salmon and Kallisto to simply say that they quantify transcripts. (I note that Salmon, in contrast to Kallisto, is described as a quasi-aligner, rather than a pseudo-aligner. I have no idea if these are really different things!)

[tbooth]

"If you know about the Kallisto software..." make no such assumption. Explain, not presume presumptuous.

I do not understand this comment.

[cmeesters]

What I mean: If you say or write "If you know about ..." you implicitly assume that people know about this feature or software. What if they do not know about this?

When I made this mistake, more often than not, I realized that attendees were at risk of loosing track.

[tbooth]

I think in this case we have the opposite. The purpose of the callout is to anticipate a question that may be asked by a small percentage of learners who are previously familiar with Kallisto and wonder why it is being run on the individual samples. If the learner does not know about the Kallisto software they are unlikely to ask this question. The assumption of the course is always that learners are familiar with some underlying ideas (short reads, RNA-Seq, mapping, alignment, assembly, etc.) but not the specific tools.

The callout does need fixing though. It promises that "we'll come back to this later in the course", but that was in the input functions chapter which was already removed.

On a more general note, @cmeesters, I do appreciate you replying to these individual issues but don't feel that you have to. I'm working through your many suggestions and requests and once I'm done I'll formulate a full response and properly ask for clarification on anything that isn't clear. If I write something curt like "don't understand" or "makes no sense" in a comment here that's a note to myself to check further or ask for clarification. I'm trying to fix the smaller issues quickly as I go but also to plan some larger changes in response to your review, and this is going to take me a few weeks. I'll keep putting comments into these issues as I go - at times they may just start to look like my stream of consciousness, or a place for me to record a commentary on the ideas I'm working on and the commits I'm making.