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/reads/fastcat_stats/per-file-stats.tsv	A TSV with per file read stats, including all samples.	aggregated
Read stats	fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv	A TSV with per read stats, including all samples.	aggregated
Run ID's	fastq_ingress_results/reads/fastcat_stats/run_ids	List of run IDs present in reads.	aggregated
Meta map json	fastq_ingress_results/reads/metamap.json	Metadata used in workflow presented in a JSON.	aggregated
Concatenated sequence data	fastq_ingress_results/reads/{{ alias }}.fastq.gz	Per sample reads concatenated in to one FASTQ file.	per-sample
Assembled transcriptome	{{ alias }}_transcriptome.fas	Per sample assembled transcriptome.	per-sample
Annotated assembled transcriptome	{{ alias }}_merged_transcriptome.fas	Per sample annotated assembled transcriptome.	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
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
Fusion transcript sequences	/jaffal_output_{{ alias }}/jaffa_results.fasta	Fusion transcript sequences output by Jaffa.	per-sample
Fusion transcript sequence summary file	/jaffal_output_{{ alias }}/jaffa_results.csv	Fusion transcript sequences summary file output by Jaffa.	per-sample