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  • Is my cuffcompare output reasonable?

    I've run cuffcompare for the first time and am wondering if my results are reasonable?

    Here are the stats:
    # Cuffcompare v1.3.0 | Command line was:
    #cuffcompare -r /home/RNAseq_tests/HG19_files/genes.gtf -o ./hacat /home/RNAseq_tests/HACAT_GATK_out_5_10/hac_cuff_5_13_no_guide/transcripts.gtf
    #

    #= Summary for dataset: /home/RNAseq_tests/HACAT_GATK_out_5_10/hac_cuff_5_13_no_guide/transcripts.gtf :
    # Query mRNAs : 43266 in 24345 loci (39462 multi-exon transcripts)
    # (8452 multi-transcript loci, ~1.8 transcripts per locus)
    # Reference mRNAs : 43294 in 24356 loci (39548 multi-exon)
    # Corresponding super-loci: 23251
    #--------------------| Sn | Sp | fSn | fSp
    Base level: 100.0 100.0 - -
    Exon level: 99.9 100.0 100.0 100.0
    Intron level: 99.8 99.8 100.0 100.0
    Intron chain level: 99.8 100.0 100.0 100.0
    Transcript level: 99.8 99.8 100.0 100.0
    Locus level: 100.0 100.0 100.0 100.0

    Matching intron chains: 39471
    Matching loci: 24345

    Missed exons: 12/238147 ( 0.0%)
    Novel exons: 0/238101 ( 0.0%)
    Missed introns: 403/218193 ( 0.2%)
    Novel introns: 0/218191 ( 0.0%)
    Missed loci: 8/24356 ( 0.0%)
    Novel loci: 0/24345 ( 0.0%)

    Total union super-loci across all input datasets: 24345


    And I've run my own statistics to find percentages of "=", "j", etc classes:

    Of 108753 entries

    43069 match the complete intron train (0.396%) [=]

    8964 were identified as novel transcripts (0.082%) [j]

    Of these 3777(0.421%) were identified as belonging to novel genes [j, FMI=100]

    25358 fragments were found within known introns (0.288%) [i]

    31337 were identified as fragments or other (0.288%) [all else]


    I'm questioning my results, mostly because of the high number of intronic fragments. My hope is that someone with a more refined eye might be able to tell me if this looks "normal", "strange", etc.


    Thanks!
    -Jeremy

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