AlexsLemonade / AlexsLemonade/refinebio
Normalization and processing options for RNA-seq data (when no cross-technology aggregation occurs )
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
### Context
Discussions around species-level compendia #508
### Problem or idea
Related to some discussion on #82
If a user is downloading experiments comprised entirely of RNA-seq data, there are a number of different ways that they might like to receive their data:
* transcript-level counts
* transcript-level TPM (transcripts per million)
* gene-level counts
* gene-level TPM
* gene-level count-scale data that takes into account library size and avg tx length (`lengthScaledTPM`)*
* the `tximport` output (`countsFromAbundance = 'no'`) as serialized R object (`.RDS`) that can be used with `DESeq2`
Additionally, users may or may not want their data normalized using quantiles from the microarray reference distribution.*
*We are set up to quantile normalize the `lengthScaledTPM` output from `tximport`. Our thought was that this is a good starting point for building compendia.
### Solution or next step
This is an area where more user research is required, as it will depend on what folks use for downstream analysis. We should also think about _how_ we would design for these options.
### New Issue Checklist
- [x] The title is short and descriptive.
- [x] You have explained the context that led you to write this issue.
- [x] You have reported a problem or idea.
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Contributor guide
No contributing guide indexed for this repository
Research direction
No files, tests, or entry points are identified. Review discussions in #508 and #82 and gather the requested user research to define supported RNA-seq outputs and normalization choices; done means an agreed design and implementation scope.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- r
- Domain
- bioinformatics, data
- Issue type
- Feature
- Difficulty
- 5/5
- Estimated time
- Over a week
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100