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AlexsLemonade / training-modules

A collection of modules that are combined into 1-5 day workshops on computational topics for the childhood cancer research community.
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Run two gastric samples for bulk RNA-seq #368

Open cbethell opened 3 years ago

cbethell commented 3 years ago

Related to a bullet point from this comment on the potential bulk RNA-seq changes inspired by 2020 May and 2020 June trainings issue #240,

We should run two gastric samples for the bulk RNA-seq material since everyone is now similarly equipped using RStudio Server, and participants would typically have more than one sample that they want to process, thus giving them a better starting point.

Also from that bullet point, we should consider

using a Makefile instead of a bash script for this per advice someone gave @cgreene

Edit: We should consider using Snakemake instead of a bash script.

cgreene commented 3 years ago

Probably snakemake but I don't remember this 😂

jaclyn-taroni commented 3 years ago

A later comment on the issue being broken up was essentially "Josh said to use snakemake instead."

cbethell commented 3 years ago

A later comment on the issue being broken up was essentially "Josh said to use snakemake instead."

Ah yes:

Forgot to note that during some discussion @jashapiro thinks Snakemake in the absence of wildcards is easier to learn than Make

That comment appeared to be a bit lonesome to me at first glance and I forgot to take another whack at connecting it to its related point before closing that issue. Updating the original comment on this issue 👍