AlexsLemonade / AlexsLemonade/refinebio

Dataset request SRP148632

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dataset request
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

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