RNA-Seq QC report
-----------------------------------

>>>>>>> Input

    bam file = /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/preprocessed/star/Touchdome_1/Touchdome_1Aligned.sortedByCoord.out.bam
    gff file = /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/supporting_files/annotation/mus_musculus/grcm38_gencode_M25/data/gencode.vM25.basic.annotation.filtered.gtf
    counting algorithm = uniquely-mapped-reads
    protocol = strand-specific-forward


>>>>>>> Reads alignment

    reads aligned  = 75,422,705
    total alignments = 81,259,438
    secondary alignments = 5,836,733
    non-unique alignments = 9,296,252
    aligned to genes  = 50,937,525
    ambiguous alignments = 416,254
    no feature assigned = 20,471,096
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  50,937,525 (71.33%)
    intronic = 15,845,065 (22.19%)
    intergenic = 4,626,031 (6.48%)
    overlapping exon = 5,412,065 (7.58%)


>>>>>>> Transcript coverage profile

    5' bias = 0.76
    3' bias = 0.46
    5'-3' bias = 1.36


>>>>>>> Junction analysis

    reads at junctions = 29,679,066

    ACCT : 5.35%
    AGGT : 4.8%
    TCCT : 4.65%
    AGGA : 3.47%
    GCCT : 2.99%
    AGCT : 2.87%
    ATCT : 2.83%
    AGGC : 2.51%
    AGGG : 2.45%
    AGAT : 2.33%
    CCCT : 2.26%