Input data and parameters
Input
| Analysis date: | Fri Apr 25 10:51:34 EDT 2025 |
| BAM file: | /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/preprocessed/star/IFE_2/IFE_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: | 66,829,685 |
| Total number of alignments: | 72,456,922 |
| Number of secondary alignments: | 5,627,237 |
| Number of non-unique alignments: | 9,090,161 |
| Aligned to genes: | 46,982,107 |
| Ambiguous alignments: | 405,274 |
| No feature assigned: | 15,864,451 |
| Missing chromosome in annotation: | 114,929 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 46,982,107 / 74.76% |
| Intronic: | 10,619,028 / 16.9% |
| Intergenic: | 5,245,423 / 8.35% |
| Intronic/intergenic overlapping exon: | 4,767,259 / 7.59% |
Transcript coverage profile
| 5' bias: | 0.71 |
| 3' bias: | 0.42 |
| 5'-3' bias: | 1.36 |
Junction analysis
| Reads at junctions: | 26,858,711 |
| ACCT | 5.28% |
| TCCT | 4.74% |
| AGGT | 4.56% |
| AGGA | 3.39% |
| GCCT | 3.09% |
| AGCT | 2.75% |
| ATCT | 2.67% |
| AGGC | 2.56% |
| AGGG | 2.49% |
| CCCT | 2.28% |
| AGAT | 2.22% |
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