Publish isoforms table
This commit is contained in:
Neil Horner
parent
84dbafd1c9
commit
fdb938a147
@ -11,6 +11,7 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
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- `de_analysis/all_counts_filtered.tsv` to `de_analysis/filtered_transcript_counts_with_genes.tsv`
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- `de_analysis/de_tpm_transcript_counts.tsv` to `de_analysis/unfiltered_tpm_transcript_counts.tsv`
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### Added
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- Published isoforms table to output directory.
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- Output additional `de_analysis/cpm_gene_counts.tsv` with counts per million gene counts.
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- Output additional `de_analysis/unfiltered_transcript_counts_with_genes.tsv` with unfiltered transcript counts with associated gene IDs.
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- Add gene name column to the de_analysis counts TSV files.
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31
README.md
31
README.md
@ -201,21 +201,22 @@ Output files may be aggregated including information for all samples or provided
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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 their probability of showing 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 transcript usage 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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| 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 |
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| 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 |
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| 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 |
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| 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 |
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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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| 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 |
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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 transcript usage 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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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
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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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68
bin/workflow_glue/make_isoform_table.py
Executable file
68
bin/workflow_glue/make_isoform_table.py
Executable file
@ -0,0 +1,68 @@
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#!/usr/bin/env python
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"""Make report tables and data for plotting."""
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from pathlib import Path
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import numpy as np
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import pandas as pd
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from .util import wf_parser # noqa: ABS101
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def argparser():
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"""Argument parser for entrypoint."""
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parser = wf_parser("Prepare report data")
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parser.add_argument(
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'--sample_id', help="Sample ID", required=True)
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parser.add_argument(
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'--gffcompare_dir',
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help="The gffcompare output directory",
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required=False,
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type=Path)
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return parser
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def make_isoform_table(gffcompare_dir, sample_id):
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"""Make an isoform summary table."""
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try:
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tmap_file = next(gffcompare_dir.glob('*.tmap'))
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except StopIteration:
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raise ValueError("Cannot find .tmap file in {}".format(gffcompare_dir))
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dtypes = {
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'ref_gene_id': str,
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'ref_id': str,
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'class_code': str,
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'qry_id': str,
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'num_exons': np.uint16,
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'cov': np.uint32,
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'len': np.uint32
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}
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df = pd.read_csv(
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tmap_file, sep='\t+',
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index_col=None,
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usecols=list(dtypes.keys()),
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dtype=dtypes)
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if len(df) == 0: # No transcripts. Write a header only result file
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df = pd.DataFrame(
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columns=list(dtypes.keys()) + ['sample_id', 'parent gene iso num'])
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df.to_csv(f'{sample_id}_transcripts_table.tsv', sep='\t', index=False)
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else:
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df = df.assign(sample_id=sample_id)
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# Make a column of number of isoforms in parent gene
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gb = df.groupby(['ref_gene_id']).count()
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gb.rename(columns={'ref_id': 'num_isoforms'}, inplace=True)
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df['parent gene iso num'] = df.apply(
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lambda x: gb.loc[(x.ref_gene_id), 'num_isoforms'], axis=1)
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# Unclassified transcripts should not be lumped together
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df.loc[df.class_code == 'u', 'parent gene iso num'] = None
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df.to_csv(f'{sample_id}_transcripts_table.tsv', sep='\t', index=False)
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def main(args):
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"""Entry point."""
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if args.gffcompare_dir:
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make_isoform_table(args.gffcompare_dir, args.sample_id)
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@ -59,6 +59,9 @@ def argparser():
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parser.add_argument(
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"--sample_ids", required=True, nargs='+',
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help="List of sample ids")
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parser.add_argument(
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"--isoform_table", required=False, type=Path,
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help="Path to directory of TSV files with isoform summaries")
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parser.add_argument(
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"--isoform_table_nrows", required=False, type=int, default=5000,
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help="Maximum rows to display in isoforms table")
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@ -549,8 +552,6 @@ def gff_compare_plots(report, gffcompare_outdirs, sample_ids):
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cover_panel = Tabs(tabs=tabs)
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section.plot(cover_panel)
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return df_tmap
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def pychopper_plots(report, pychop_report):
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"""Make plots from pychopper output.
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@ -648,11 +649,10 @@ def cluster_quality(cluster_qc_dir, report, sample_ids):
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section.plot(cover_panel)
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def transcript_table(report, df_tmaps, max_rows):
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def transcript_table(report, isoform_table, max_rows):
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"""Create searchable table of transcripts.
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:param df_tmaps: pd.DataFrame of all gffcomapre `.tmap` files from all
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samples
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:param isoform_table: path to folder of isoform table files
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"""
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section = report.add_section()
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@ -668,24 +668,11 @@ def transcript_table(report, df_tmaps, max_rows):
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`isoform_table_nrows`. It is currently set to `{}`
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'''.format(max_rows))
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df = df_tmaps.drop(
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columns=[
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'FPKM', 'qry_gene_id', 'major_iso_id', 'ref_match_len', 'TPM'])
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if len(df) == 0:
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sys.stderr("No transcripts found")
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section.markdown("No transcripts found")
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return
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# Make a column of number of isoforms in parent gene
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gb = df.groupby(['ref_gene_id', 'sample_id']).count()
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# gb = gb.set_index(['ref_gene_id', 'sample_id'])
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gb.rename(columns={'ref_id': 'num_isoforms'}, inplace=True)
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df['parent gene iso num'] = df.apply(
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lambda x: gb.loc[(x.ref_gene_id, x.sample_id), 'num_isoforms'], axis=1)
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# Uncalssified transcritps should not be lumped togetehr
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df.loc[df.class_code == 'u', 'parent gene iso num'] = None
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dfs = []
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for file_ in Path(isoform_table).iterdir():
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d = pd.read_csv(file_, sep='\t')
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dfs.append(d)
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df = pd.concat(dfs)
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# Keep top n rows with most coverage
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df.sort_values('cov', ascending=False, inplace=True)
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@ -934,14 +921,13 @@ def main(args):
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report, args.gff_annotation, sample_ids)
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if args.gffcompare_dir is not None:
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df_tmaps = gff_compare_plots(
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gff_compare_plots(
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report,
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[Path(x) for x in args.gffcompare_dir],
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sample_ids)
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if df_tmaps is not None:
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# Skip this section. This needs some work
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transcript_table(report, df_tmaps, args.isoform_table_nrows)
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if args.isoform_table is not None:
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transcript_table(report, args.isoform_table, args.isoform_table_nrows)
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if args.cluster_qc_dirs is not None:
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cluster_quality(args.cluster_qc_dirs, report, sample_ids)
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@ -12,18 +12,19 @@ Output files may be aggregated including information for all samples or provided
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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 their probability of showing 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 transcript usage 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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| 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 |
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| 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 |
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| 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 |
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| 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 |
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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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| 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 |
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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 transcript usage 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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| 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 |
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| 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 |
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| 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 |
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| 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 |
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| 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](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml) | per-sample |
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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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28
main.nf
28
main.nf
@ -303,8 +303,11 @@ process run_gffcompare{
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tuple val(sample_id), path(query_annotation)
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path ref_annotation
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output:
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tuple val(sample_id), path("${sample_id}_gffcompare"), emit: gffcmp_dir
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path ("${sample_id}_annotated.gtf"), emit: gtf, optional: true
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tuple val(sample_id), path("${sample_id}_gffcompare"),
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emit: gffcmp_dir
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path ("${sample_id}_annotated.gtf"), emit: gtf
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tuple val(sample_id), path("${sample_id}_transcripts_table.tsv"),
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emit: isoforms_table
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script:
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def out_dir = "${sample_id}_gffcompare"
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"""
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@ -320,6 +323,11 @@ process run_gffcompare{
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mv *.tmap $out_dir
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mv *.refmap $out_dir
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cp ${out_dir}/str_merged.annotated.gtf ${sample_id}_annotated.gtf
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# Make an isoform table for report and user output.
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workflow-glue make_isoform_table \
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--sample_id $sample_id \
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--gffcompare_dir "${sample_id}_gffcompare"
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"""
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}
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@ -379,7 +387,6 @@ process merge_transcriptomes {
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"""
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}
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process makeReport {
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label "isoforms"
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@ -398,6 +405,7 @@ process makeReport {
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path "gff_annotation/*"
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path "de_report/*"
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path "seqkit/*"
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path "isoforms_table/*"
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output:
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path("wf-transcriptomes-*.html"), emit: report
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// for DE analysis, a `gene_name` column will be added to
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@ -439,6 +447,11 @@ process makeReport {
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else
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OPT_PC_REPORT="--pychop_report pychopper_report/*"
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fi
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if [ -f "isoforms_table/OPTIONAL_FILE" ]; then
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OPT_ISO_TABLE=""
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else
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OPT_ISO_TABLE="--isoform_table isoforms_table"
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fi
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workflow-glue report --report !{report_name} \
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--versions !{versions} \
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--params params.json \
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@ -447,6 +460,7 @@ process makeReport {
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--sample_ids !{sids} \
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--stats per_read_stats/* \
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${OPT_GFF_ANNOTATION} \
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${OPT_ISO_TABLE} \
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${OPT_GFFCMP_DIR} \
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--isoform_table_nrows !{params.isoform_table_nrows} \
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${OPT_JAFFAL_CSV} \
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@ -598,6 +612,7 @@ workflow pipeline {
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run_gffcompare(merge_gff_bundles.out.gff, ref_annotation)
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gff_compare_dir = run_gffcompare.out.gffcmp_dir
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gff_compare = run_gffcompare.out.gffcmp_dir.map{ it -> it[1]}.collect()
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isoforms_table = run_gffcompare.out.isoforms_table.map{ it -> it[1]}.collect()
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// create per sample gff tuples with gff compare directories
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gff_tuple = merge_gff_bundles.out.gff
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.join(gff_compare_dir)
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@ -606,6 +621,7 @@ workflow pipeline {
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optional_channel = Channel.fromPath("$projectDir/data/OPTIONAL_FILE")
|
||||
gff_tuple = merge_gff_bundles.out.gff.combine(optional_channel)
|
||||
gff_compare = OPTIONAL_FILE
|
||||
isoforms_table = file("$projectDir/data/OPTIONAL_FILE")
|
||||
}
|
||||
// For reference based assembly, there is only one reference
|
||||
// So map this reference to all sample_ids
|
||||
@ -620,6 +636,7 @@ workflow pipeline {
|
||||
}
|
||||
else{
|
||||
gff_compare = file("$projectDir/data/OPTIONAL_FILE")
|
||||
isoforms_table = file("$projectDir/data/OPTIONAL_FILE")
|
||||
merge_gff = file("$projectDir/data/OPTIONAL_FILE")
|
||||
assembly_stats = file("$projectDir/data/OPTIONAL_FILE")
|
||||
use_ref_ann = false
|
||||
@ -632,7 +649,6 @@ workflow pipeline {
|
||||
jaffal_out = file("$projectDir/data/OPTIONAL_FILE")
|
||||
}
|
||||
|
||||
|
||||
if (params.de_analysis){
|
||||
sample_sheet = file(params.sample_sheet, type:"file")
|
||||
if (!params.ref_transcriptome){
|
||||
@ -670,7 +686,8 @@ workflow pipeline {
|
||||
gff_compare,
|
||||
merge_gff,
|
||||
de_report,
|
||||
count_transcripts_file)
|
||||
count_transcripts_file,
|
||||
isoforms_table)
|
||||
|
||||
report = makeReport.out.report
|
||||
|
||||
@ -679,6 +696,7 @@ workflow pipeline {
|
||||
if (use_ref_ann){
|
||||
results = run_gffcompare.output.gffcmp_dir.concat(
|
||||
assembly.stats,
|
||||
run_gffcompare.out.isoforms_table,
|
||||
get_transcriptome.out.transcriptome.flatMap(map_sample_ids_cls))
|
||||
.map {it -> it[1]}
|
||||
.concat(results)
|
||||
|
||||
@ -81,7 +81,7 @@
|
||||
"type": "per-sample"
|
||||
},
|
||||
"dge-results-tsv": {
|
||||
"filepath": "/de_analysis/results_dge.tsv",
|
||||
"filepath": "de_analysis/results_dge.tsv",
|
||||
"title": "Differential gene expression results",
|
||||
"description": "This is a gene-level result file that describes genes and their probability of showing differential expression between experimental conditions.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -89,7 +89,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"dge-report-pdf": {
|
||||
"filepath": "/de_analysis/results_dge.pdf",
|
||||
"filepath": "de_analysis/results_dge.pdf",
|
||||
"title": "Differential gene expression report",
|
||||
"description": "Summary report of differential gene expression analysis as a PDF.",
|
||||
"mime-type": "application/pdf",
|
||||
@ -97,7 +97,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"dtu-gene-tsv": {
|
||||
"filepath": "/de_analysis/results_dtu_gene.tsv",
|
||||
"filepath": "de_analysis/results_dtu_gene.tsv",
|
||||
"title": "Differential transcript usage gene TSV",
|
||||
"description": "This is a gene-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -105,7 +105,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"dtu-report-pdf": {
|
||||
"filepath": "/de_analysis/results_dtu.pdf",
|
||||
"filepath": "de_analysis/results_dtu.pdf",
|
||||
"title": "Differential transcript usage report",
|
||||
"description": "Summary report of differential transcript usage results as a PDF.",
|
||||
"mime-type": "application/pdf",
|
||||
@ -113,7 +113,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"dtu-transcript": {
|
||||
"filepath": "/de_analysis/results_dtu_transcript.tsv",
|
||||
"filepath": "de_analysis/results_dtu_transcript.tsv",
|
||||
"title": "Differential transcript usage TSV",
|
||||
"description": "This is a transcript-level result file from DEXSeq that lists annotated genes and their probabilities of differential expression.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -121,7 +121,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"dtu-stageR": {
|
||||
"filepath": "/de_analysis/results_dtu_stageR.tsv ",
|
||||
"filepath": "de_analysis/results_dtu_stageR.tsv ",
|
||||
"title": "Differential transcript usage stageR TSV",
|
||||
"description": "This is the output from StageR and it shows both gene and transcript probabilities of differential expression",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -129,7 +129,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"dexseq": {
|
||||
"filepath": "/de_analysis/results_dexseq.tsv",
|
||||
"filepath": "de_analysis/results_dexseq.tsv",
|
||||
"title": "Differential transcript usage DEXSeq TSV",
|
||||
"description": "The complete output from the DEXSeq-analysis, shows both gene and transcript probabilities of differential expression.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -137,7 +137,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"gene_counts": {
|
||||
"filepath": "/de_analysis/all_gene_counts.tsv",
|
||||
"filepath": "de_analysis/all_gene_counts.tsv",
|
||||
"title": "Gene counts",
|
||||
"description": "Raw gene counts created by the Salmon tool, before filtering.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -145,7 +145,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"gene_counts_per_million": {
|
||||
"filepath": "/de_analysis/cpm_gene_counts.tsv",
|
||||
"filepath": "de_analysis/cpm_gene_counts.tsv",
|
||||
"title": "Gene counts per million",
|
||||
"description": "This file shows counts per million (CPM) of the raw gene counts to facilitate comparisons across samples.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -153,7 +153,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"transcript_counts": {
|
||||
"filepath": "/de_analysis/unfiltered_transcript_counts_with_genes.tsv",
|
||||
"filepath": "de_analysis/unfiltered_transcript_counts_with_genes.tsv",
|
||||
"title": "Transcript counts",
|
||||
"description": "Raw transcript counts created by the Salmon tool, before filtering. Includes reference to the associated gene ID.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -161,7 +161,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"tpm_transcript_counts": {
|
||||
"filepath": "/de_analysis/unfiltered_tpm_transcript_counts.tsv",
|
||||
"filepath": "de_analysis/unfiltered_tpm_transcript_counts.tsv",
|
||||
"title": "Transcript per million counts",
|
||||
"description": "This file shows transcripts per million (TPM) of the raw counts to facilitate comparisons across samples.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
@ -169,15 +169,23 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"transcipt_counts_filtered": {
|
||||
"filepath": "/de_analysis/filtered_transcript_counts_with_genes.tsv",
|
||||
"filepath": "de_analysis/filtered_transcript_counts_with_genes.tsv",
|
||||
"title": "Transcript counts filtered",
|
||||
"description": "Filtered transcript counts, used for differential transcript usage analysis. Includes a reference to the associated gene ID.",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
"optional": true,
|
||||
"type": "aggregated"
|
||||
},
|
||||
"transcripts_table": {
|
||||
"filepath": "{{ alias }}_transcripts_table.tsv",
|
||||
"title": "Transcript info table",
|
||||
"description": "This file details each isoform that was reconstructed from the input reads. It contains a subset of columns from the .tmap output from [gffcompare](https://ccb.jhu.edu/software/stringtie/gffcompare.shtml)",
|
||||
"mime-type": "text/tab-separated-values",
|
||||
"optional": true,
|
||||
"type": "per-sample"
|
||||
},
|
||||
"final_non_redundant_transcriptome": {
|
||||
"filepath": "/de_analysis/final_non_redundant_transcriptome.fasta",
|
||||
"filepath": "de_analysis/final_non_redundant_transcriptome.fasta",
|
||||
"title": "Final non redundant transcriptome",
|
||||
"description": "Transcripts that were used for differential expression analysis including novel transcripts with the identifiers used for DE analysis.",
|
||||
"mime-type": "text/x-fasta",
|
||||
@ -185,7 +193,7 @@
|
||||
"type": "aggregated"
|
||||
},
|
||||
"jaffa_fasta": {
|
||||
"filepath": "/jaffal_output_{{ alias }}/jaffa_results.fasta",
|
||||
"filepath": "jaffal_output_{{ alias }}/jaffa_results.fasta",
|
||||
"title": "Fusion transcript sequences",
|
||||
"description": "Fusion transcript sequences output by Jaffa.",
|
||||
"mime-type": "text/x-fasta",
|
||||
@ -193,7 +201,7 @@
|
||||
"type": "per-sample"
|
||||
},
|
||||
"jaffa_results": {
|
||||
"filepath": "/jaffal_output_{{ alias }}/jaffa_results.csv",
|
||||
"filepath": "jaffal_output_{{ alias }}/jaffa_results.csv",
|
||||
"title": "Fusion transcript sequence summary file",
|
||||
"description": "Fusion transcript sequences summary file output by Jaffa.",
|
||||
"mime-type": "text/csv",
|
||||
|
||||
Loading…
Reference in New Issue
Block a user