AlexsLemonade / AlexsLemonade/refinebio
Dataset request SRP148632
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
### Context
A user requested [SRP148632](https://www.refine.bio/experiments/SRP148632/genome-wide-transcriptome-analysis-of-the-model-of-transient-focal-ischemia-in-rat-brain)
### Problem or idea
SRP148632 is a rat RNA-seq experiment with 12 total samples and no downloadable samples.
### Solution or next step
A cursory glance at some of the samples yields:
```
Salmon timed out because it failed to complete within 3 hours.
```
Not sure if that is specific for the `quant` step or the entire pipeline and therefore could come up as a single sample failing = no `tximport` step.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start with the SRP148632 experiment linked in the issue and inspect the samples reporting that Salmon timed out after three hours. Determine whether the timeout occurs during quantification or blocks the full pipeline and tximport step; the issue is done when the affected samples are downloadable or the failure scope is clearly documented.
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
- 30/100