Run two gastric samples for bulk RNA-seq
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Nobody has claimed this yet.
Assessment
- Difficulty
- 5/5
- Estimated time
- Over a week
- Newbie friendliness
- 25/100
- Issue type
- Feature
- Clarity
- Needs clarification
- Activity status
- Stale
- Tech stack
- bash, r
- Domain
- bioinformatics
Research direction
Start with the linked comment and issue #240 to understand the proposed bulk RNA-seq changes. The issue mentions running two gastric samples and replacing the bash script with either a Makefile or Snakemake, but names no files or tests. Done means the training material supports the agreed sample count and workflow approach.
Written by the indexing model from the issue text.
Description
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.
- Dominant language
- HTML
- Stars
- 80
- Forks
- 35
- Avg merge
- 5h 54m
- Merged PRs (30d)
- 19
Getting set up
- Ships a Dockerfile or Docker Compose file
- No pull request template
- Read the contributing guide
First steps
- Read the whole issue, then the project's contributing guide.
- Comment on the issue to say you are picking it up — it saves two people doing the same work.
- Fork the repository and make your change on a branch.
- Open a pull request that references the issue number.
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