Question: Differential abundance of 15 genes in metagenomic sample.
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gravatar for mdurrant
5 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 4 months ago by Asaf4.8k • written 5 months ago by mdurrant10
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gravatar for Asaf
4 months ago by
Asaf4.8k
Israel
Asaf4.8k 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 4 months ago by Asaf4.8k

In other words, you can use RTqPCR.

ADD REPLYlink written 4 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 4 months ago by Asaf4.8k
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