Input data and parameters
Input
| Analysis date: | Fri Apr 25 10:51:55 EDT 2025 |
| 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 |
| 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: | 50,739,757 |
| Total number of alignments: | 54,243,028 |
| Number of secondary alignments: | 3,503,271 |
| Number of non-unique alignments: | 5,586,491 |
| Aligned to genes: | 35,136,141 |
| Ambiguous alignments: | 289,259 |
| No feature assigned: | 13,157,372 |
| Missing chromosome in annotation: | 73,765 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 35,136,141 / 72.76% |
| Intronic: | 10,331,350 / 21.39% |
| Intergenic: | 2,826,022 / 5.85% |
| Intronic/intergenic 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% |
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