Normalization in DESeq
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Entering edit mode
7.7 years ago
Whoknows ▴ 890

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

HTSeq DESeq RNA-Seq Tophat • 2.3k views
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Entering edit mode
7.7 years ago

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

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