griffithlab / griffithlab/pVACtools
Spot check transcript vs. gene expression values from kallisto
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- Dominant language
- Python
- Stars
- 188
- Forks
- 81
- Avg merge
- 9d 17h
- Merged PRs (30d)
- 6
Description
In pVACview we noticed that the transcript values rarely add up to something close to the gene value (which is almost always quite a bit higher).
We should double check the right numbers are being pulled in?
If so, maybe back up and look at the upstream step in the rna-seq pipeline to make sure tximport is doing the right thing?
Contributor guide
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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.
Research direction
Start by tracing how pVACview pulls transcript and gene expression values from kallisto results, then inspect the upstream RNA-seq pipeline step involving tximport. Compare the values at each stage to determine whether the discrepancy is in pVACview or the pipeline; done means identifying the source of the mismatch and defining the required correction.
Written by the indexing model from the issue text.
Assessment
- Tech stack
- python
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 35/100