Understanding Homer output for makeTagDirectory
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3 months ago
Assa Yeroslaviz ★ 1.8k

I was wondering where I can find explanation about the output given to me by homer's makeTagDirectory command.

one of the files return this output:

        Optimizing tag files...
        Estimated genome size = 4227865
        Estimated average read density = 1.741583 per bp
        Total Tags = 7363177.0
        Total Positions = 11846383
        Average tag length = 175.6
        Median tags per position = 0 (ideal: 4)
        Average tags per position = 0.197                                                                 <=? 
        Fragment Length Estimate: 191
        Peak Width Estimate: 0                                                                            <=?
                !!! No reliable estimate for peak size
                Setting Peak width estimate to be equal to fragment length estimate
        Autocorrelation quality control metrics:
                Same strand fold enrichment: 1.0
                Diff strand fold enrichment: 1.0
                Same / Diff fold enrichment: 1.0

                Guessing sample is ChIP-Seq - may have low enrichment with lots of background

        Forcing fragment length = -123456

How do I interpret these results? Is it correct to assume here, that the ChIP-seq experiment wasn't really successful? or why do i get this message at the ensd?

chip-seq peaks homer makeTagDirectory • 195 views
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