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  • 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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