Question: DeSEQ normalization for knockout
0
gravatar for langya
16 months ago by
langya40
langya40 wrote:

Hey

I have two different knockout (knockout of different genes), and one negative controls (all knockout by CRISPR Cas9 SYSTEM). First i normalized my knockout to the negative controls to see what genes are differentially expressed between WT and knockout by using deseq. Now I want to compare what genes are differentially expressed between my knockout, can i take the DeSEQ output directly to compare or what should I do? How does the normalization in DESEQ work? [The normalization to negative control is necessary because I do not want to see the changes that are purely cause by CRISPR system. ]

sequencing rna-seq next-gen • 621 views
ADD COMMENTlink modified 16 months ago by Fabio Marroni2.1k • written 16 months ago by langya40
1
gravatar for Fabio Marroni
16 months ago by
Fabio Marroni2.1k
Italy
Fabio Marroni2.1k wrote:

The best option is to feed ALL of your raw counts to DESeq2 and normalize all the data together. DESeq2 (and if I well remember DESeq as well) has options to perform analysis when you have more than two levels (treated and control). You can find some mention of it at the paragraph "Contrasts" of the DESeq2 manual

ADD COMMENTlink written 16 months ago by Fabio Marroni2.1k
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