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Release v0.5.3
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@Maarten-vd-Sande Maarten-vd-Sande released this 03 Jun 13:12
v0.5.3
dcdffd8

Automated preprocessing of Next-Generation Sequencing data, including full (sc)ATAC-seq, ChIP-seq, and RNA-seq workflows.

Added

  • DESeq2 blind sample distance & correlation cluster heatmaps for RNA-, ATAC- ChIP-seq counts
    • find them annotated in the MultiQC when running >1 sample

Changed

  • "biological_replicate" and "technical_replicate" renamed to *"_replicates" (matches between samples.tsv & config.yaml)
  • fixed bug with seq2science making a {output.allsizes} file
  • Changed explain to use 'passive style'
  • Genrich peak calling defaults
    • Doesn't remove PCR duplicates anymore (best to do with markduplicates)
    • Changed extsize to 200 to be similar to macs settings
    • Turned off tn5 shift, since that is done by seq2science

Fixed

  • depend less on local genomes (only when data is unavailable online)
  • trackhub explanation was missing, added
  • bug with broad peaks and qc that could not be made
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