Input data and parameters
Input
| Analysis date: | Fri Apr 25 10:56:31 EDT 2025 |
| BAM file: | /sc/arion/projects/BiNGS/bings_omics/data/bings/2025/bulk_course_data/bulkrna_pipeline/data_rna/preprocessed/star/IFE_3/IFE_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: | 142,635,553 |
| Total number of alignments: | 154,046,430 |
| Number of secondary alignments: | 11,410,877 |
| Number of non-unique alignments: | 17,996,805 |
| Aligned to genes: | 102,092,447 |
| Ambiguous alignments: | 809,612 |
| No feature assigned: | 32,931,423 |
| Missing chromosome in annotation: | 216,143 |
| Not aligned: | 0 |
Reads genomic origin
| Exonic: | 102,092,447 / 75.61% |
| Intronic: | 26,093,080 / 19.32% |
| Intergenic: | 6,838,343 / 5.06% |
| Intronic/intergenic overlapping exon: | 10,657,779 / 7.89% |
Transcript coverage profile
| 5' bias: | 0.79 |
| 3' bias: | 0.47 |
| 5'-3' bias: | 1.3 |
Junction analysis
| Reads at junctions: | 58,897,281 |
| ACCT | 5.35% |
| AGGT | 4.68% |
| TCCT | 4.58% |
| AGGA | 3.42% |
| GCCT | 3.09% |
| AGCT | 2.85% |
| ATCT | 2.75% |
| AGGC | 2.44% |
| AGGG | 2.41% |
| CCCT | 2.3% |
| AGAT | 2.27% |
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