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_3/Touchdome_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  = 50,739,757
    total alignments = 54,243,028
    secondary alignments = 3,503,271
    non-unique alignments = 5,586,491
    aligned to genes  = 35,136,141
    ambiguous alignments = 289,259
    no feature assigned = 13,157,372
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  35,136,141 (72.76%)
    intronic = 10,331,350 (21.39%)
    intergenic = 2,826,022 (5.85%)
    overlapping exon = 4,031,124 (8.35%)


>>>>>>> Transcript coverage profile

    5' bias = 0.77
    3' bias = 0.46
    5'-3' bias = 1.36


>>>>>>> Junction analysis

    reads at junctions = 21,318,400

    ACCT : 5.35%
    AGGT : 4.72%
    TCCT : 4.64%
    AGGA : 3.44%
    GCCT : 2.94%
    AGCT : 2.93%
    ATCT : 2.79%
    AGGC : 2.49%
    AGGG : 2.43%
    CCCT : 2.32%
    AGAT : 2.31%