wf-transcriptomes-v202/docs/08_outputs.md

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 }}.

Title	File path	Description	Per sample or aggregated
Workflow report	wf-transcriptomes-report.html	HTML report summarising transcript discovery, quantification, optional SQANTI3 classification, and optional differential analysis results.	aggregated
Per-file read stats	ingress_results/{{ alias }}/fastcat_stats/per-file-stats.tsv	Read statistics for each input FASTQ file in a sample, when FASTQ read stats are available.	per-sample
Per-read stats	ingress_results/{{ alias }}/fastcat_stats/per-read-stats.tsv.gz	Read statistics for individual reads in a sample, when this output is enabled.	per-sample
Ingress reads	ingress_results/{{ alias }}/seqs.fastq.gz	Reads prepared from the input data for downstream analysis.	per-sample
Ingress metadata	ingress_results/{{ alias }}/metamap.json	Per-sample metadata used by the workflow.	per-sample
Aligned BAM	samples/{{ alias }}/alignment/reads.bam	Genome-aligned BAM used for bambu, optional SQANTI3 QC, and IGV.	per-sample
Aligned BAM index	samples/{{ alias }}/alignment/reads.bam.bai	Index for the aligned BAM.	per-sample
Alignment summary	samples/{{ alias }}/alignment/bamstats.flagstat.tsv	bamstats flagstat summary for the aligned BAM.	per-sample
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
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
Cohort transcriptome GTF	cohort/transcripts.gtf	Joint bambu transcript model used as the primary cohort transcriptome.	aggregated
Cohort transcriptome FASTA	cohort/cohort.transcriptome.fa	Transcript sequences derived from the joint cohort GTF.	aggregated
Cohort transcript counts	cohort/transcript_counts.tsv	Transcript-level count matrix produced by bambu.	aggregated
Cohort gene counts	cohort/gene_counts.tsv	Gene-level count matrix derived from bambu output.	aggregated
Cohort transcript metadata	cohort/transcript_metadata.tsv	Transcript annotations and bambu transcript classes for the cohort model.	aggregated
Cohort SQANTI3 summary	cohort/sqanti_cohort/classification_summary.tsv	SQANTI3 classification summary for the cohort transcriptome when SQANTI3 QC is enabled.	aggregated
Per-sample transcriptome GTF	samples/{{ alias }}/transcripts.gtf	Independent bambu transcript model for an individual sample.	per-sample
Per-sample transcriptome FASTA	samples/{{ alias }}/{{ alias }}.transcriptome.fa	Transcript sequences derived from the per-sample GTF.	per-sample
Per-sample transcript counts	samples/{{ alias }}/transcript_counts.tsv	Transcript-level abundance estimates for the per-sample bambu model.	per-sample
Per-sample gene counts	samples/{{ alias }}/gene_counts.tsv	Gene-level abundance estimates for the per-sample bambu model.	per-sample
Per-sample transcript metadata	samples/{{ alias }}/transcript_metadata.tsv	Transcript annotations and bambu transcript classes for the per-sample model.	per-sample
Per-sample SQANTI3 summary	samples/{{ alias }}/{{ alias }}_sqanti/classification_summary.tsv	SQANTI3 classification summary for the per-sample transcriptome when SQANTI3 QC is enabled.	per-sample
Differential gene expression results	de_analysis/{{ contrast }}/results_dge.tsv	DESeq2 gene-level differential expression results for one contrast.	aggregated
Differential gene expression plots	de_analysis/{{ contrast }}/results_dge.pdf	PDF plots generated during DESeq2 analysis for one contrast.	aggregated
Differential transcript usage results	de_analysis/{{ contrast }}/results_dtu_transcript.tsv	Transcript-level DTU results for one contrast.	aggregated
Differential transcript usage gene summary	de_analysis/{{ contrast }}/results_dtu_gene.tsv	Gene-level DTU summary for one contrast.	aggregated
DEXSeq results	de_analysis/{{ contrast }}/results_dexseq.tsv	Full DEXSeq result table for one contrast.	aggregated
Differential transcript usage plots	de_analysis/{{ contrast }}/results_dtu.pdf	PDF plots generated during DEXSeq analysis for one contrast.	aggregated
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
Differential analysis text summary	de_analysis/de_overall_summary.txt	Human-readable DE/DTU run summary across all contrasts.	aggregated
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
DESeq2 fallback diagnostic	de_analysis/DESeq2_dispersion_fallback_{{ contrast }}.txt	Diagnostic details when DESeq2 falls back to gene-wise dispersion estimation.	aggregated
DTU failure diagnostic	de_analysis/{{ contrast }}/DTU_ANALYSIS_FAILED.txt	Diagnostic details when DEXSeq fails for a contrast.	aggregated
Multiple-testing warning	de_analysis/MULTIPLE_TESTING_WARNING.txt	Family-wise error-rate note generated when multiple contrasts are tested.	aggregated
IGV configuration	igv.json	JSON configuration for viewing the aligned BAMs in IGV.	aggregated
Reference FASTA index	igv_reference/{{ ref_genome_file }}.fai	FAI index for the reference genome published for IGV.	aggregated
Reference GZI index	igv_reference/{{ ref_genome_file }}.gzi	GZI index for a compressed reference genome published for IGV.	aggregated