Input data and parameters
Input
| Analysis date: | Fri Apr 25 10:53:13 EDT 2025 |
| BAM file: | /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/preprocessed/star/IFE_1/IFE_1Aligned.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: | 87,479,467 |
| Total number of alignments: | 93,844,220 |
| Number of secondary alignments: | 6,364,753 |
| Number of non-unique alignments: | 10,073,871 |
| Aligned to genes: | 62,546,916 |
| Ambiguous alignments: | 483,640 |
| No feature assigned: | 20,610,920 |
| Missing chromosome in annotation: | 128,873 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 62,546,916 / 75.21% |
| Intronic: | 16,097,606 / 19.36% |
| Intergenic: | 4,513,314 / 5.43% |
| Intronic/intergenic overlapping exon: | 6,447,581 / 7.75% |
Transcript coverage profile
| 5' bias: | 0.78 |
| 3' bias: | 0.48 |
| 5'-3' bias: | 1.3 |
Junction analysis
| Reads at junctions: | 37,057,873 |
| ACCT | 5.35% |
| AGGT | 4.72% |
| TCCT | 4.61% |
| AGGA | 3.47% |
| GCCT | 3.02% |
| AGCT | 2.9% |
| ATCT | 2.79% |
| AGGC | 2.48% |
| AGGG | 2.42% |
| AGAT | 2.32% |
| CCCT | 2.32% |
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