42 lines
6.2 KiB
Markdown
42 lines
6.2 KiB
Markdown
Output files may be aggregated including information for all samples or provided per sample. Per-sample files will be prefixed with respective aliases and represented below as {{ alias }}.
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| Title | File path | Description | Per sample or aggregated |
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|-------|-----------|-------------|--------------------------|
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| Workflow report | wf-transcriptomes-report.html | HTML report summarising transcript discovery, quantification, SQANTI3 classification, and optional differential analysis results. | aggregated |
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| Aligned BAM | samples/{{ alias }}/alignment/reads.bam | Genome-aligned BAM used for bambu, SQANTI3 QC, and IGV. | per-sample |
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| Aligned BAM index | samples/{{ alias }}/alignment/reads.bam.bai | Index for the aligned BAM. | per-sample |
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| Alignment summary | samples/{{ alias }}/alignment/bamstats.flagstat.tsv | bamstats flagstat summary for the aligned BAM. | per-sample |
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| Modified base pileup | samples/{{ alias }}/mods/{{ alias }}.mods.bedmethyl.gz | Per-sample modkit bedMethyl pileup generated from the aligned BAM when MM and ML tags are present. | per-sample |
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| Modified base summary | samples/{{ alias }}/mods/{{ alias }}.mods.summary.tsv | Per-sample global modification-percent summary aggregated from the modkit bedMethyl pileup, with one row per modification code. | per-sample |
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| Modified base bigWig | samples/{{ alias }}/mods/{{ alias }}.mods.*.bw | Per-sample modkit bigWig tracks generated from the aligned BAM, with one file per requested or inferred modification code. | per-sample |
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| Reference and annotation preparation summary | cohort/reference/annotation_reference_summary.json | Summary of reference and annotation preparation, including seqname overlap, build/provider hints, and excluded unstranded annotation counts. | aggregated |
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| Excluded unstranded annotation records | cohort/reference/unstranded_annotation.gtf | Full set of annotation records excluded because their strand was not '+' or '-'. Present only when unstranded records are found. | aggregated |
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| Cohort transcriptome GTF | cohort/transcripts.gtf | Joint bambu transcript model used as the primary cohort transcriptome. | aggregated |
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| Cohort transcriptome FASTA | cohort/cohort.transcriptome.fa | Transcript sequences derived from the joint cohort GTF. | aggregated |
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| Cohort transcript counts | cohort/transcript_counts.tsv | Transcript-level count matrix produced by bambu. | aggregated |
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| Cohort gene counts | cohort/gene_counts.tsv | Gene-level count matrix derived from bambu output. | aggregated |
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| Cohort transcript metadata | cohort/transcript_metadata.tsv | Transcript annotations and bambu transcript classes for the cohort model. | aggregated |
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| Cohort SQANTI3 summary | cohort/sqanti/classification_summary.tsv | SQANTI3 classification summary for the cohort transcriptome. | aggregated |
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| Per-sample transcriptome GTF | samples/{{ alias }}/transcripts.gtf | Independent bambu transcript model for an individual sample. | per-sample |
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| Per-sample transcriptome FASTA | samples/{{ alias }}/{{ alias }}.transcriptome.fa | Transcript sequences derived from the per-sample GTF. | per-sample |
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| Per-sample transcript counts | samples/{{ alias }}/transcript_counts.tsv | Transcript-level abundance estimates for the per-sample bambu model. | per-sample |
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| Per-sample gene counts | samples/{{ alias }}/gene_counts.tsv | Gene-level abundance estimates for the per-sample bambu model. | per-sample |
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| Per-sample transcript metadata | samples/{{ alias }}/transcript_metadata.tsv | Transcript annotations and bambu transcript classes for the per-sample model. | per-sample |
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| Per-sample SQANTI3 summary | samples/{{ alias }}/sqanti/classification_summary.tsv | SQANTI3 classification summary for the per-sample transcriptome. | per-sample |
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| Differential gene expression results | de_analysis/{{ contrast }}/results_dge.tsv | DESeq2 gene-level differential expression results for one contrast. | aggregated |
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| Differential gene expression plots | de_analysis/{{ contrast }}/results_dge.pdf | PDF plots generated during DESeq2 analysis for one contrast. | aggregated |
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| Differential transcript usage results | de_analysis/{{ contrast }}/results_dtu_transcript.tsv | Transcript-level DTU results for one contrast. | aggregated |
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| Differential transcript usage gene summary | de_analysis/{{ contrast }}/results_dtu_gene.tsv | Gene-level DTU summary for one contrast. | aggregated |
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| DEXSeq results | de_analysis/{{ contrast }}/results_dexseq.tsv | Full DEXSeq result table for one contrast. | aggregated |
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| Differential transcript usage plots | de_analysis/{{ contrast }}/results_dtu.pdf | PDF plots generated during DEXSeq analysis for one contrast. | aggregated |
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| Differential analysis QC summary | de_analysis/de_qc_stats.json | Structured DE/DTU QC summary. Use analysis_fallbacks for aggregate counts, and each contrast's deseq2_dispersion_fallback, dexseq_dispersion_method, and dexseq_covariates_dropped fields for interpretation. | aggregated |
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| Differential analysis text summary | de_analysis/de_overall_summary.txt | Human-readable DE/DTU run summary across all contrasts. | aggregated |
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| Per-contrast QC summary | de_analysis/{{ contrast }}/contrast_qc_summary.txt | Human-readable per-contrast DE/DTU QC summary including sample counts and key significance totals. | aggregated |
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| DESeq2 fallback diagnostic | de_analysis/DESeq2_dispersion_fallback_{{ contrast }}.txt | Diagnostic details when DESeq2 falls back to gene-wise dispersion estimation. | aggregated |
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| DGE failure diagnostic | de_analysis/{{ contrast }}/DGE_ANALYSIS_FAILED.txt | Diagnostic details when DESeq2 fails for a contrast. | aggregated |
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| DTU failure diagnostic | de_analysis/{{ contrast }}/DTU_ANALYSIS_FAILED.txt | Diagnostic details when DEXSeq fails for a contrast. | aggregated |
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| Multiple-testing warning | de_analysis/MULTIPLE_TESTING_WARNING.txt | Family-wise error-rate note generated when multiple contrasts are tested. | aggregated |
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| IGV configuration | igv.json | JSON configuration for viewing the aligned BAMs in IGV. | aggregated |
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| Reference FASTA index | reference/{{ ref_genome_file }}.fai | FAI index for the reference genome published for IGV. | aggregated |
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| Reference GZI index | reference/{{ ref_genome_file }}.gzi | GZI index for a compressed reference genome published for IGV. | aggregated |
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