Input data and parameters
Input
| Analysis date: | Fri Apr 25 10:50:18 EDT 2025 |
| BAM file: | /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/preprocessed/star/HF_2/HF_2Aligned.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: | 41,059,693 |
| Total number of alignments: | 43,711,256 |
| Number of secondary alignments: | 2,651,563 |
| Number of non-unique alignments: | 4,269,342 |
| Aligned to genes: | 28,912,626 |
| Ambiguous alignments: | 236,285 |
| No feature assigned: | 10,229,512 |
| Missing chromosome in annotation: | 63,491 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 28,912,626 / 73.87% |
| Intronic: | 8,113,175 / 20.73% |
| Intergenic: | 2,116,337 / 5.41% |
| Intronic/intergenic overlapping exon: | 2,900,439 / 7.41% |
Transcript coverage profile
| 5' bias: | 0.74 |
| 3' bias: | 0.47 |
| 5'-3' bias: | 1.34 |
Junction analysis
| Reads at junctions: | 16,716,678 |
| ACCT | 5.35% |
| AGGT | 4.78% |
| TCCT | 4.54% |
| AGGA | 3.46% |
| AGCT | 3.02% |
| GCCT | 2.88% |
| ATCT | 2.62% |
| AGGC | 2.55% |
| AGAT | 2.42% |
| CCCT | 2.39% |
| AGGG | 2.36% |
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