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Old 09-10-2018, 12:55 PM   #1
sganesh02
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Location: CDC,Atlanta, GA

Join Date: Feb 2012
Posts: 1
Default Dealing with low read count in some samples

Greeting Members

I have an experiment with 4 time points and 5 biological replicates and each biological replicate has 5 technical replicates (100 samples thus)

The first two time points are really early is the organism's life cycle and hence we often expect less reads for some genes:

After summing the reads from the technical replicates, I get this profile (OBVIOUSLY AN ARTEFACT)
0h GeneA 3 reads
0h GeneA 2 reads
0h GeneA 0 reads
0h GeneA 1 reads
0h GeneA 3 reads

24h GeneA 0 reads
24h GeneA 1 reads
24h GeneA 2 reads
24h GeneA 0 reads
24h GeneA 1 reads

But DeSeq2 analysis of DE of these genes gives me a profile like this:
baseMean log2FoldChange lfcSE stat pvalue padj
31.88739159 -4.026822896 0.943450084 -4.268188603 1.97E-05 0.007173227

How do I filter for such artefacts ? Though I give an example here, my results are severely afflicted with these kind of low read count but highly significant statistics.
Any suggestion is highly appreciated...

I cannot set a minreadcount filter as these genes will have higher read count as the time line progresses (and will also skew the stats if I only remove it for one time point)
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