Input data and parameters
Input
| Analysis date: | Fri Apr 25 10:51:47 EDT 2025 |
| BAM file: | /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/preprocessed/star/Touchdome_2/Touchdome_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: | 48,629,248 |
| Total number of alignments: | 52,148,257 |
| Number of secondary alignments: | 3,519,009 |
| Number of non-unique alignments: | 5,687,239 |
| Aligned to genes: | 34,094,186 |
| Ambiguous alignments: | 289,163 |
| No feature assigned: | 12,009,187 |
| Missing chromosome in annotation: | 68,482 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 34,094,186 / 73.95% |
| Intronic: | 8,612,616 / 18.68% |
| Intergenic: | 3,396,571 / 7.37% |
| Intronic/intergenic overlapping exon: | 3,678,112 / 7.98% |
Transcript coverage profile
| 5' bias: | 0.77 |
| 3' bias: | 0.47 |
| 5'-3' bias: | 1.27 |
Junction analysis
| Reads at junctions: | 20,500,390 |
| ACCT | 5.42% |
| AGGT | 4.66% |
| TCCT | 4.63% |
| AGGA | 3.42% |
| GCCT | 3% |
| AGCT | 2.84% |
| ATCT | 2.81% |
| AGGC | 2.53% |
| AGGG | 2.47% |
| AGAT | 2.3% |
| CCCT | 2.27% |
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