htseq counts normalization

Question

[mxlsherry1992]

Hi,

I have used STAR-HTseq-DEseq to do the RNA seq analysis and differential expression analysis, but except, now I need to do normalization for the counts from HTseq ( using for other software), if you have any idea for that?

The counts got from HTseq is like this: I only put an example here, pan21, pan22 are two replicates, and pan41, pan42 are other replicates.

gene_id         pan21   pan22   pan41   pan42
gene-LOC113538309   0   0   9   3
gene-LOC113538979   26  11  28  34
gene-ndrg4  344 451 210 443
gene-fam114a1   172 212 57  55
gene-LOC113539788   3   2   8   6
gene-LOC113539787   56  48  15  34
gene-LOC113539784   58  46  15  28
gene-hcn4   40  64  13  26
gene-LOC113538848   0   1   0   3
gene-LOC113539780   50  54  19  32
gene-dennd4b    147 174 60  98
gene-LOC113539250   740 1004    604 1733
gene-LOC113539251   9   11  26  38
gene-ano3   32  50  26  64
gene-LOC113539253   119 159 76  226
gene-LOC113539254   126 118 83  256
gene-dennd4a    244 253 141 218
gene-LOC113539256   5854    7709    2591    2853
gene-LOC113539258   109 150 82  128
gene-ano8   90  97  35  60
gene-abtb2  96  128 34  37
gene-abtb1  79  101 41  86

Thank you!

Answer 1

[igor]

If you already did differential expression, you should already have normalized counts. You can extract them from your DESeq object with counts(dds, normalized=TRUE). You can see an example here: https://hbctraining.github.io/DGE_workshop/lessons/02_DGE_count_normalization.html

[mxlsherry1992]

I will try it!! Thank u!