29 lines
4.1 KiB
Markdown
29 lines
4.1 KiB
Markdown
Outputs 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 | a HTML report document detailing the primary findings of the workflow | aggregated |
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| 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 |
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| Per file read stats | fastq_ingress_results/reads/fastcat_stats/per-read-stats.tsv | A TSV with per read stats, including all samples. | aggregated |
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| Run ID's | fastq_ingress_results/reads/fastcat_stats/run_ids | List of run IDs present in reads. | aggregated |
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| Meta map json | fastq_ingress_results/reads/metamap.json | Metadata used in workflow presented in a JSON. | aggregated |
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| Concatenated sequence data | fastq_ingress_results/reads/{{ alias }}.fastq.gz | Per sample reads concatenated in to one FASTQ file. | per-sample |
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| Assembled transcriptome | {{ alias }}_transcriptome.fas | Per sample assembled transcriptome. | per-sample |
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| Annotated assembled transcriptome | {{ alias }}_merged_transcriptome.fas | Per sample annotated assembled transcriptome. | per-sample |
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| Alignment summary statistics | {{ alias }}_read_aln_stats.tsv | Per sample alignment summary statistics. | per-sample |
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| GFF compare results. | {{ alias }}_gffcompare | All GFF compare output files. | per-sample |
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| Differential gene expression results | /de_analysis/results_dge.tsv | This is a gene-level result file that describes genes and the probability that they show differential expression between experimental conditions . | aggregated |
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| Differential gene expression report | /de_analysis/results_dge.pdf | Summary report of differential gene expression analysis as a PDF. | aggregated |
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| 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 |
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| Differential gene expression report | /de_analysis/results_dtu.pdf | Summary report of differential transcript usage results as a PDF. | aggregated |
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| 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 |
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| 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 |
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| 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 |
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| Gene counts | /de_analysis/all_gene_counts.tsv | Raw gene counts created by the Salmon tool, before filtering. | aggregated |
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| Transcript counts | /de_analysis/all_transcript_counts.tsv | Raw transcript counts created by the Salmon tool, before filtering. | aggregated |
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| Transcript counts filtered | /de_analysis/all_counts_filtered.tsv | Filtered transcript counts, used for DE_analysis. | aggregated |
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| Transcript per million counts | /de_analysis/de_tpm_transcript_counts.tsv | This file shows transcript per million (TPM) of the raw counts to facilitate comparisons across sample. | aggregated |
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| 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 |
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| Fusion transcript sequences | /jaffal_output_{{ alias }}/jaffa_results.fasta | Fusion transcript sequences output by Jaffa. | per-sample |
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| Fusion transcript sequence summary file | /jaffal_output_{{ alias }}/jaffa_results.csv | Fusion transcript sequences summary file output by Jaffa. | per-sample |
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