seq2science

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

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

• "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

• 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