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foerstner-lab / READemption

A pipeline for the computational evaluation of RNA-Seq data
https://reademption.readthedocs.io
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Which normalization from gene_quanti is used for Deseq2? #58

Open termithorbor opened 7 months ago

termithorbor commented 7 months ago

Hi, Which normalization method from the gene_quanti output is used for the Deseq2 analysis? Is there a way to change which normalization approach is used for the Desq2 analysis? Thanks in advance.

Tillsa commented 7 months ago

Hi, The DESeq2 subcommand automatically takes the raw counts from the gene quanti step and there is no option to use normalized counts, since DESeq2 requires raw counts as input. Best wishes, Till