wf-transcriptomes-v202/docs/07_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	a HTML report document detailing the primary findings of the workflow	aggregated
Per file read stats	fastq_ingress_results/{{ alias }}//reads/fastcat_stats/per-file-stats.tsv	A TSV with per file read stats, including all samples.	aggregated
Read stats	fastq_ingress_results/{{ alias }}//reads/fastcat_stats/per-read-stats.tsv	A TSV with per read stats, including all samples.	aggregated
Run ID's	fastq_ingress_results/{{ alias }}//reads/fastcat_stats/run_ids	List of run IDs present in reads.	aggregated
Meta map json	fastq_ingress_results/{{ alias }}//reads/metamap.json	Metadata used in workflow presented in a JSON.	aggregated
Concatenated sequence data	fastq_ingress_results/{{ alias }}//reads/{{ alias }}.fastq.gz	Per sample reads concatenated in to one FASTQ file.	per-sample
Assembled transcriptome	{{ alias }}_transcriptome.fas	Per sample assembled transcriptome. Not output if a reference annotation was supplied	per-sample
Annotated assembled transcriptome	{{ alias }}_merged_transcriptome.fas	Per sample annotated assembled transcriptome. Only output if a reference annotation was supplied	per-sample
Alignment summary statistics	{{ alias }}_read_aln_stats.tsv	Per sample alignment summary statistics.	per-sample
GFF compare results.	{{ alias }}_gffcompare	All GFF compare output files.	per-sample
Differential gene expression results	de_analysis/results_dge.tsv	This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions.	aggregated
Differential gene expression report	de_analysis/results_dge.pdf	Summary report of differential gene expression analysis as a PDF.	aggregated
Differential transcript usage gene TSV	de_analysis/results_dtu_gene.tsv	This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.	aggregated
Differential transcript usage report	de_analysis/results_dtu.pdf	Summary report of differential transcript usage results as a PDF.	aggregated
Differential transcript usage TSV	de_analysis/results_dtu_transcript.tsv	This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.	aggregated
Differential transcript usage stageR TSV	de_analysis/results_dtu_stageR.tsv	This is the output from StageR and it shows both gene and transcript probabilities of differential expression	aggregated
Differential transcript usage DEXSeq TSV	de_analysis/results_dexseq.tsv	The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression.	aggregated
Gene counts	de_analysis/all_gene_counts.tsv	Raw gene counts created by the Salmon tool, before filtering.	aggregated
Gene counts per million	de_analysis/cpm_gene_counts.tsv	This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples.	aggregated
Transcript counts	de_analysis/unfiltered_transcript_counts_with_genes.tsv	Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID.	aggregated
Transcript per million counts	de_analysis/unfiltered_tpm_transcript_counts.tsv	This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples.	aggregated
Transcript counts filtered	de_analysis/filtered_transcript_counts_with_genes.tsv	Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID.	aggregated
Transcript info table	{{ alias }}_transcripts_table.tsv	This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from gffcompare	per-sample
Final non redundant transcriptome	de_analysis/final_non_redundant_transcriptome.fasta	Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis.	aggregated
Index of reference FASTA file	igv_reference/{{ ref_genome file }}.fai	Reference genome index of the FASTA file required for IGV config.	aggregated
GZI index of the reference FASTA file	igv_reference/{{ ref_genome file }}.gzi	GZI Index of the reference FASTA file.	aggregated
JSON configuration file for IGV browser	igv.json	JSON configuration file to be loaded in IGV for visualising alignments against the reference.	aggregated
BAM file (minimap2)	BAMS/{{ alias }}.reads_aln_sorted.bam	BAM file generated from mapping input reads to the reference.	per-sample
BAM index file (minimap2)	BAMS/{{ alias }}.reads_aln_sort.bam.bai	Index file generated from mapping input reads to the reference.	per-sample