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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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merge samples in kallisto_quant step #16

Open dlaehnemann opened 4 years ago

dlaehnemann commented 4 years ago

This PR implements sample merging by providing kallisto with all the units of a sample at once. I.e. if multiple sequencing runs are provided for a sample as units, kallisto will jointly quantify abundance for all the runs. In addition, the workflow now checks whether units of a sample are either all paired end or all single end and throws an exception if this is violated for a sample.

johanneskoester commented 4 years ago

The implementation is fine. I am just wondering if this is really what one wants to do. If units are just unmerged lanes, then yes. If they are technical replicates, then probably no. Let us have a chat about this when I am in the office on Thursday.

dlaehnemann commented 4 years ago

Sure, let's discuss further. My first instinct would be for technical replicates to be modelled via the batch variables...