AlexsLemonade / AlexsLemonade/refinebio

Dataset Request SRP141691

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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 [`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

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