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_2/Touchdome_2Aligned.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  = 48,629,248
    total alignments = 52,148,257
    secondary alignments = 3,519,009
    non-unique alignments = 5,687,239
    aligned to genes  = 34,094,186
    ambiguous alignments = 289,163
    no feature assigned = 12,009,187
    not aligned = 0


>>>>>>> Reads genomic origin

    exonic =  34,094,186 (73.95%)
    intronic = 8,612,616 (18.68%)
    intergenic = 3,396,571 (7.37%)
    overlapping exon = 3,678,112 (7.98%)


>>>>>>> Transcript coverage profile

    5' bias = 0.77
    3' bias = 0.47
    5'-3' bias = 1.27


>>>>>>> Junction analysis

    reads at junctions = 20,500,390

    ACCT : 5.42%
    AGGT : 4.66%
    TCCT : 4.63%
    AGGA : 3.42%
    GCCT : 3%
    AGCT : 2.84%
    ATCT : 2.81%
    AGGC : 2.53%
    AGGG : 2.47%
    AGAT : 2.3%
    CCCT : 2.27%