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Published February 13, 2024 | Version v1.1.0
Software Open

epi2me-labs/wf-transcriptomes: v1.1.0

Authors/Creators

  • 1. @Birkbeck
  • 2. Oxford Nanopore Technologies
  • 3. @nanoporetech
  • 4. @nanoporetech, @epi2me-labs

Description

Changed

  • Improve documentation around filtering of transcripts done before DTU analysis.
  • Renamed files:
    • de_analysis/all_counts_filtered.tsv to de_analysis/filtered_transcript_counts_with_genes.tsv
    • de_analysis/de_tpm_transcript_counts.tsv to de_analysis/unfiltered_tpm_transcript_counts.tsv
  • Minimum memory requirements to 32 GB.

Added

  • Published isoforms table to output directory.
  • Output additional de_analysis/cpm_gene_counts.tsv with counts per million gene counts.
  • Output additional de_analysis/unfiltered_transcript_counts_with_genes.tsv with unfiltered transcript counts with associated gene IDs.
  • Add gene name column to the de_analysis counts TSV files.

Fixed

  • Mapping stage using a single thread only.

Changed

  • More memory assigned to the fusion detection process.
  • When no --ref_annotation is provided the workflow will still run but the output transcripts will not be annotated. However --de_analysis mode still requires a --ref_annotation.

Files

epi2me-labs/wf-transcriptomes-v1.1.0.zip

Files (124.4 MB)

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md5:42217c5447877af51211f4bfd6a688a2
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Additional details

Related works

Is supplement to
Software: https://github.com/epi2me-labs/wf-transcriptomes/tree/v1.1.0 (URL)

Software

Repository URL
https://github.com/epi2me-labs/wf-transcriptomes