Question: Differential abundance of 15 genes in metagenomic sample.
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gravatar for mdurrant
11 months ago by
mdurrant10
mdurrant10 wrote:

Say you have two metagenomic samples. You want to quantify the differential abundance of 15 genes between the two samples. What's the most straight-forward way to do this, while properly accounting for the sequencing depth of each library?

ADD COMMENTlink modified 10 months ago by Asaf5.0k • written 11 months ago by mdurrant10
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gravatar for Asaf
10 months ago by
Asaf5.0k
Israel
Asaf5.0k wrote:

You'll have to find a normalizing gene, a gene that should have the same levels in both samples. It would be very hard to normalize otherwise. Another approach is to have conclusions in the form: gene A is more abundant than gene B in sample 1 (or condition 1) but less in sample 2. It would be much stronger if you'll look at pathways or modules etc.

ADD COMMENTlink written 10 months ago by Asaf5.0k

In other words, you can use RTqPCR.

ADD REPLYlink written 10 months ago by theobroma221.1k

If it's just 15 genes of interest then sure, I was hoping he would want to get some more out of this data :)

ADD REPLYlink written 10 months ago by Asaf5.0k
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