AlexsLemonade / AlexsLemonade/refinebio

Dataset Request SRP149884

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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 [SRP149884](https://www.refine.bio/experiments/SRP149884/non-inflammatory-tumor-microenvironment-of-diffuse-intrinsic-pontine-glioma-dipg).

### Problem or idea

It looks like Salmon timed out on a good number of the samples.

### Solution or next step

Try running it locally. This could be related to the issue I fixed where the number of reads wasn't being identified correctly.

Contributor guide

No contributing guide indexed for this repository

Research direction

Start by attempting to run dataset SRP149884 locally with Salmon and record which samples time out. Compare the behavior with the earlier fix for incorrect read-count identification; done means determining whether that fix resolves the failures or confirming a separate cause.

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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