Input data and parameters
Input
| Analysis date: | Fri Apr 25 10:52:12 EDT 2025 |
| 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 |
| Counting algorithm: | uniquely-mapped-reads |
| GTF 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 |
| Paired-end sequencing: | no |
| Protocol: | strand-specific-forward |
| Sorting performed: | no |
Summary
Reads alignment
| Number of mapped reads: | 70,654,861 |
| Total number of alignments: | 75,845,524 |
| Number of secondary alignments: | 5,190,663 |
| Number of non-unique alignments: | 8,350,808 |
| Aligned to genes: | 49,046,773 |
| Ambiguous alignments: | 408,913 |
| No feature assigned: | 17,948,838 |
| Missing chromosome in annotation: | 90,192 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 49,046,773 / 73.21% |
| Intronic: | 14,331,187 / 21.39% |
| Intergenic: | 3,617,651 / 5.4% |
| Intronic/intergenic 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% |
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