base_level and level_of_interest in example config.yaml

snakemake-workflows / rna-seq-star-deseq2

RNA-seq workflow using STAR and DESeq2

MIT License

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base_level and level_of_interest in example config.yaml #73

Closed keksundso closed 7 months ago

keksundso commented 9 months ago

In the diffexp section of the example config.yaml the two variables _baselevel and _level_ofinterest are set to A, B, and C, which are the sample names defined in samples.tsv.

However, shouldn't the level refer to the treatment_# column of samples.tsv, thus in the example files 'treated' or 'untreated'. (e.g. like in the .test/configs)

dlaehnemann commented 7 months ago

Thanks for reporting this and sorry, if this caused confusion in the setup.

I updated the example config/config.yaml accordingly. But do feel free to double-check that everything is correct now. :sweat_smile: