seq2science

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

Version 0.5.0 brings many quality of life improvements, such as seq2science automatically inferring what needs to be re-run when changing the samples.tsv and/or the config.yaml, differential peak analysis for chip/atac workflows and tab-completion!

To (hopefully) clear things up we changed the way technical and biological replicates are called, now technical and biological replicate, before technical replicate and condition.

It is important to note that the RNA-seq workflow DOES NOT remove duplicate reads anymore as a default, and that the sc/bulk ATAC-seq workflows now filters reads on the nucleosome-free region as a default.

• Keep all duplicate reads in RNA-seq by default
• Slimmed down the config printed at the start of a run
• Changed some rules into localrules when executed on a cluster
• moved onehot peaks to counts_dir
• DESeq2 contrasts now accept any column names
  • groups still cannot contain underscores
  • no longer accepts one group name
  • more examples added to the docs!

• dupRadar module to analyse read duplication types in RNA-seq
• Differential peak analysis for ATAC- and ChIP-seq!
• Options to filter bams by minimum and maximum insert sizes (added to config of bulk/sc atac)
• Support experiment ids for EBI ENA and DDBJ for downloading public samples
• More robust expression handling for BUS format detection from kb-python arguments
• Short-hand BUS syntax for indrop v1/v2
• Seq2science now supports tab-completion
• Seq2science now outputs a logfile in the directory it is run

• renamed more old "replicate" variables to the new "technical_replicate"
• minor logging tweak
• Chipseeker now works without defining descriptive name column
• fix bug in resources parsing of profiles
• small bug when naming a column condition in non peak-calling workflows