Normalization in DESeq

Question

[Whoknows]

Hi friends

I tried to normalize my count table in DESeq which SizeFactor of them are:

    N1      S1               S2
0.9936395   0.9606483    1.0525232

It happened because S2 has much more aligned reads (in bam file) in contrast with other 2 samples.

What should I do to normalize S2 in DESeq? How can I use normalization to make them close?

Thanks

Answer 1

[Devon Ryan]

DESeq (you should be using DESeq2) will take care of that for you.