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biowdl/RNA-seq: Release 5.0.0

integration_instructionsResearch softwarekeyboard_double_arrow_right Software 16 Jul 2021Publisher:Zenodo

Authors: Ruben Vorderman; Davy Cats; Peter van 't Hof; Jasper; Leon Mei; Cedrick Agaser; Tom Kuipers;

doi: 10.5281/zenodo.3459256 , 10.5281/zenodo.5109461

biowdl/RNA-seq: Release 5.0.0

- Summary
- Related research
  (2)
- Metrics

Abstract

Update default CPAT version to 3.0.4. Use gffcompare to merge stringtie assembly GTF files, rather than stringtie merge. Add call to create annotation file for shiny app. Add call to create design matrix template for shiny app. Add predex v0.9.2 container to dockerImages. dockerImages.yml: update umitools (v1.1.1) image with correct version of samtools (1.10). test/cromwell_options.json: add memory attribute. dockerImages.yml: update umitools to version 1.1.1 (multi-package including samtools). Replace travis with github CI. Add the dockerImages to the output section. Make running stringtie optional by exposing the boolean runStringtieQuantification. Downgrade stringtie to version 1.3.6, as version 2 returns unstranded transcripts which is incompatible with htseq-count. When multiple TPM/FPKM values are returned for a single gene by stringtie, they will now be added together in the multi-sample expression tables. Previously only the last value encountered would be used. Updated default docker image for collect-columns (now uses version 1.0.0 instead of 0.2.0).

Related Organizations

Leiden University Medical Center
Netherlands

2 Research products, page 1 of 1

biowdl/RNA-seq: v1.0.0
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biowdl/RNA-seq: Release 2.0.0
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Impact byBIP!

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	popularity This indicator reflects the "current" impact/attention (the "hype") of an article in the research community at large, based on the underlying citation network.	Average
	influence This indicator reflects the overall/total impact of an article in the research community at large, based on the underlying citation network (diachronically).	Average
	impulse This indicator reflects the initial momentum of an article directly after its publication, based on the underlying citation network.	Average