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/HF_3/HF_3Aligned.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  = 70,654,861
    total alignments = 75,845,524
    secondary alignments = 5,190,663
    non-unique alignments = 8,350,808
    aligned to genes  = 49,046,773
    ambiguous alignments = 408,913
    no feature assigned = 17,948,838
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  49,046,773 (73.21%)
    intronic = 14,331,187 (21.39%)
    intergenic = 3,617,651 (5.4%)
    overlapping exon = 5,228,309 (7.8%)


>>>>>>> Transcript coverage profile

    5' bias = 0.77
    3' bias = 0.48
    5'-3' bias = 1.34


>>>>>>> Junction analysis

    reads at junctions = 27,689,960

    ACCT : 5.37%
    AGGT : 4.75%
    TCCT : 4.36%
    AGGA : 3.45%
    AGCT : 3.02%
    GCCT : 2.9%
    ATCT : 2.59%
    AGGC : 2.52%
    AGAT : 2.38%
    CCCT : 2.38%
    AGGG : 2.38%