galaxyproject / galaxyproject/training-material

Transcriptomics training 'RNAseq - counts to genes' - incorrect data in Shared Data

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paper-cut transcriptomics
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Description

Related tutorial: https://training.galaxyproject.org/training-material/topics/transcriptomics/tutorials/rna-seq-counts-to-genes/tutorial.html

TLDR: Shared Data link to import files is incorrect, need to use provided zenodo links instead. Should alter the training material markdown.

Under the 'Import Data' section, two options to upload files are given. By importing from Shared Data (GTN - Material -> transcriptomics -> 2: RNA-seq counts to genes), or by using provided zenodo links.

The zenodo links contain the **_correct data_**, while the Shared Data is in a **_different format_**. Sample IDs are different in the Shared Data count matrix, and the factordata contains 4 cols, not 2. Additionally, there are 2 factordata files in the same folder, but have conflicting entries for some samples.

Grace :)

Contributor guide

Open the contributing guide

Research direction

Open the linked RNA-seq counts-to-genes tutorial and find its Import Data section in the training material markdown. Compare the Shared Data option with the provided Zenodo links, then update the instructions so learners use the correct data source and verify that the conflicting Shared Data files are no longer presented as alternatives.

Written by the indexing model from the issue text.

Assessment

Tech stack
markdown
Domain
documentation
Issue type
Documentation
Difficulty
1/5
Estimated time
1-3 hours
Activity status
Stale
Clarity
Clearly specified
Newbie friendliness
35/100

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