<commit_before><commit_msg>QualiMap RNAseq: add test for integer 5'/3' bias<commit_after>RNA-Seq QC report
-----------------------------------

>>>>>>> Input

    bam file = NEB_PRJ180311_2900-8052613.bam
    gff file = /data/cephfs/punim0010/local/development/bcbio/genomes/Hsapiens/GRCh37/rnaseq/ref-transcripts.gtf
    counting algorithm = proportional
    protocol = non-strand-specific


>>>>>>> Reads alignment

    reads aligned  = 343,855,552
    total alignments = 387,667,822
    secondary alignments = 43,812,270
    non-unique alignments = 0
    aligned to genes  = 189,170,706
    ambiguous alignments = 4,821,428
    no feature assigned = 193,656,578
    not aligned = 7,323,400
    SSP estimation (fwd/rev) = 0.02 / 0.98


>>>>>>> Reads genomic origin

    exonic =  189,170,706 (49.41%)
    intronic = 142,424,194 (37.2%)
    intergenic = 51,232,384 (13.38%)
    overlapping exon = 22,809,720 (5.96%)


>>>>>>> Transcript coverage profile

    5' bias = 0.74
    3' bias = 0.71
    5'-3' bias = 1


>>>>>>> Junction analysis

    reads at junctions = 64,245,042

    ACCT : 5.3%
    AGGT : 4.94%
    TCCT : 3.58%
    AGGA : 3.47%
    AGCT : 3.02%
    ATCT : 2.98%
    CCCT : 2.95%
    GCCT : 2.65%
    AGGC : 2.62%
    AGGG : 2.53%
    AGAT : 2.34%
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