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snakemake-workflows / rna-seq-kallisto-sleuth

A Snakemake workflow for differential expression analysis of RNA-seq data with Kallisto and Sleuth.
MIT License
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Plots v2 #14

Closed AntonieV closed 4 years ago

AntonieV commented 4 years ago

Implementation of volcano plot: For getting sleuth object after wald-test directly, sleuth::plot_volcano() is called in sleuth-diffexp.R script without an own snakemake-rule. For this plot it's necessary to set value of pval_aggregate of sleuth object to FALSE. Set pval_aggregate after that to TRUE again, leads to an unexpected behavior in sleuth and error message, which is reported here: https://github.com/pachterlab/sleuth/pull/240

dlaehnemann commented 4 years ago

@johanneskoester I don't have the necessary permissions to merge this, so could you? This should all be fine and reviewed---and we can add further adjustments in a new branch. But I would prefer to have this merged for now, to pull this into an actual workflow and test there --- and so that we don't end up with a diverging master...