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duplication rate reporting, mismatch #199

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bartns opened this issue Oct 7, 2019 · 1 comment
Open

duplication rate reporting, mismatch #199

bartns opened this issue Oct 7, 2019 · 1 comment

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@bartns
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bartns commented Oct 7, 2019

Dear fastp devs,

I have a high duplication rate report which does not make sense according to the graph that is generated. Duplication rate is reported as 87.6% whereas in the graph it gives a duplication rate of 1 of 91%.

How should I interpret this?

Data from the json:

"filtering_result": {
                "passed_filter_reads": 46475992,
                "low_quality_reads": 205838,
                "too_many_N_reads": 5826,
                "too_short_reads": 20906,
                "too_long_reads": 0
        },
        "duplication": {
                "rate": 0.876254,
                "histogram": [268418,10761,2802,1567,1125,890,783,669,611,506,461,436,406,350,394,346,330,301,325,280,277,277,228,240,251,247,252,227,210,204,27203],
                "mean_gc": [0.295962,0.383945,0.438027,0.462227,0.481799,0.480573,0.493627,0.490489,0.492295,0.479819,0.509778,0.491806,0.496977,0.52335,0.51704,0.495036,0.505692,0.50299,0.488989,0.506373,0.504467,0.495448,0.523099,0.533611,0.528896,0.531031,0.495254,0.498886,0.504276,0.496021,0.503588]
        },

I ran it with default settings.
(RNAseq data)
@sfchen
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sfchen commented Oct 31, 2019

91% fragments have unique reads
87.6% reads are duplicated

91% fragments have unique reads, but some fragments have many many duplicated reads (i.e. 10000 dup), and finally resulted in that 87.6% reads are duplicated.

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@sfchen @bartns