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  • High wrong/miss loci rate by assembling transcripts

    Hi All,

    I used tophat/cufflink (latest version) to assemble mouse transcripts. However, I found the cuffcompare output the very high wrong/miss loci. Do anyone has the ideas about this issue?


    #--------------------| Sn | Sp | fSn | fSp
    Base level: 56.6 53.2 - -
    Exon level: 33.6 29.6 40.9 35.9
    Intron level: 56.4 88.4 59.1 92.6
    Intron chain level: 13.3 21.1 44.0 69.6
    Transcript level: 0.0 0.0 0.4 0.1
    Locus level: 24.1 5.5 29.7 6.7
    Missed exons: 91911/319314 ( 28.8%)
    Wrong exons: 143371/363197 ( 39.5%)
    Missed introns: 72669/230224 ( 31.6%)
    Wrong introns: 5486/146922 ( 3.7%)
    Missed loci: 13301/33490 ( 39.7%)
    Wrong loci: 103823/147819 ( 70.2%)

    Total union super-loci across all datasets: 170485
    (12284 multi-transcript, ~2.2 transcripts per locus)

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