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New report format

Merged
#41 · Created  · Last updated

Merged pull request

Merged in develop (pull request #41)

  • 2b3f197
  • Author:
  • Closed by:
  • 2018-05-08

Description

  • Rewrote QC report from scratch

  • Added filtering of contaminating cells based on marker gene expression

  • Added so that you can use different references for the various RSeQC steps (mainly to be able to run `geneBody_coverage.py` on a subset of genes

  • Changed QC config structure

  • No longer built for Python 3.5 (dumping settings to yaml relies on that dicts are ordered, which was implemented in 3.6)

NOTE: The config structure regarding QC was changed in a way that's not backwards compatible. Before everything was in the root, now it's under "qc". I hope this is fine since it wasn't long ago that QC was added in the first place. See example below

1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 qc: multiqc_parse: ... filter_settings: default_sd_cut: 2 nfail: 2 filters: ... expression_filters: # Beta cells are considered those cells that don't pass any of these criteria (values in RPKM) multi-cell: ENSMUSG00000000394 > 185000 & (ENSMUSG00000004366 > 5750 | ENSMUSG00000000215 > 5750) alpha: ENSMUSG00000000394 > 185000 delta: ENSMUSG00000004366 > 5750 stellate: ENSMUSG00000026728 > 32 other_non-beta: ENSMUSG00000000215 < 5750

 

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