AlexsLemonade / AlexsLemonade/refinebio
Dataset Request SRP141691
- Dominant language
- Python
- Stars
- 135
- Forks
- 21
- PR merge metrics
- No merged PRs in 30d
Description
### Context
A user requested [`SRP141691`](https://www.refine.bio/experiments/SRP141691/cd19-mutations-found-in-cd19-negative-relapse-to-cart-19-in-all-patients).
### Problem or idea
[`SRP141691`](https://www.refine.bio/experiments/SRP141691/cd19-mutations-found-in-cd19-negative-relapse-to-cart-19-in-all-patients) has two samples that we discovered, but no downloadable samples. When we take a look at that [project at ENA](https://www.ebi.ac.uk/ena/data/view/PRJNA451298), the library layout is `SINGLE` but each run has three FASTQ files associated with it.
### Solution or next step
It could be the case that a run/sample was sequenced multiple times, maybe using different protocols or it could be the result of multiplexing. This will take more digging by a member of the science team.
Contributor guide
No contributing guide indexed for this repository
Research direction
Start by comparing the refine.bio SRP141691 page with the ENA project PRJNA451298, focusing on why two discovered samples have no downloadable samples despite a SINGLE library layout and three FASTQ files per run. Determine whether repeated sequencing, different protocols, or multiplexing explains the records, then document the finding and next step for the science team.
Written by the indexing model from the issue text.
Assessment
- Domain
- bioinformatics
- Issue type
- Bug
- Difficulty
- 4/5
- Estimated time
- 3-5 days
- Activity status
- Stale
- Clarity
- Needs clarification
- Newbie friendliness
- 25/100