Updates for RNA-Seq - Githubissues

A few updates for the SOP:

[x] Add Best Practices reference (and possibly Fig1)
[x] Require both methods for the exercise
[x] Update intro section to emphasize building up knowledge and background prior (lit review).

Per Slack w/ Faisal:

cjfields [10:07 AM] Ok One other point that might be worth thinking about. We have two alternative methods (alignment and pseudoalignment); should they know both or only be required to run one? It's not clear in the SOP. Some of the questions expect both. Most obvious: "How do counts between the two methods (alignment vs. pseudoalignment) compare?"

Faisal Fadlelmola [10:08 AM] I think it better to include both

cjfields [10:09 AM] I agree I can tweak the wording with that in mind

Faisal Fadlelmola [10:10 AM] A survey of best practices for RNA-seq data analysis this is one of the best paper we used during our assessment

cjfields [10:11 AM] Is that referenced in the SOP?

Faisal Fadlelmola [10:11 AM] no

cjfields [10:11 AM] We can easily add it I'm going to add a Github issue to track these two points (requiring both methods, adding the reference) to make sure they get done Just in case

Faisal Fadlelmola [10:13 AM] I like their Figure 1: Pasted image at 2018-10-30, 6:12 PM

cjfields [10:14 AM] Can see if that's Creative Commons, if so we could add it in as well.

Faisal Fadlelmola [10:15 AM] Citation: A survey of best practices for RNA-seq data analysis

Genome Biology, 2016, Volume 17, Number 1, Page 1 Ana Conesa, Pedro Madrigal, Sonia Tarazona, David Gomez-Cabrero, Alejandra Cervera, Andrew McPherson, Michał Wojciech Szcześniak, Daniel J. Gaffney, Laura L. Elo, Xuegong Zhang, Ali Mortazavi

h3abionet / H3ABionet-SOPs

Updates for RNA-Seq #7