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  • Does these Cuffcompare results look okay

    I aligned my RNAseq data to the mouse mm10 genome using Bowtie2. I then generated a GTF file using Cufflinks, and then used Cuffcompare to compare against an annotated mouse genome (from UCSC Table Browswer).

    # Cuffcompare v2.1.1 | Command line was:
    #/home/adam/cufflinks/cuffcompare transcripts.gtf -r refFlatMouse.gtf
    #

    #= Summary for dataset: transcripts.gtf :
    # Query mRNAs : 13129 in 13129 loci (0 multi-exon transcripts)
    # (0 multi-transcript loci, ~1.0 transcripts per locus)
    # Reference mRNAs : 30786 in 23311 loci (27576 multi-exon)
    # Corresponding super-loci: 3150
    #--------------------| Sn | Sp | fSn | fSp
    Base level: 2.5 68.1 - -
    Exon level: 0.1 2.3 1.2 20.3
    Intron level: 0.0 -nan 0.0 -nan
    Intron chain level: 0.0 -nan 0.0 -nan
    Transcript level: 0.0 0.0 0.0 0.0
    Locus level: 0.0 0.0 0.0 0.0

    Matching intron chains: 0
    Matching loci: 0

    Missed exons: 206087/216519 ( 95.2%)
    Novel exons: 2718/13129 ( 20.7%)
    Missed introns: 193970/193970 (100.0%)
    Missed loci: 20087/23311 ( 86.2%)
    Novel loci: 2718/13129 ( 20.7%)

    Total union super-loci across all input datasets: 5887

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