docs

DEEP Process Documents

Standardized pipelines per assay type

Assay	Alignment	Quantification	Comment
ChIP-seq	genome	chip-seq	6 histone modifications plus input control
DNase-seq	genome	dnase-seq	DNaseI hypersensitivity
NOMe-seq	bisulfite	nome-seq	Nucleosome occupancy and DNA methylation
(m)RNA-seq	transcriptome	transcriptome	polyA-enriched total RNA-seq (stranded)
(sn)RNA-seq	transcriptome	transcriptome	micro RNA
(t)RNA-seq	transcriptome	transcriptome	ribo-depleted total RNA-seq (stranded)
RRBS	bisulfite	bisulfite	Reduced representation bisulfite sequencing
WGBS	bisulfite	bisulfite	Whole-genome bisulfite sequencing

Non-default pipelines

The Process documents in the Interpretation folder represent non-default pipelines, i.e., they are not necessarily applied to all DEEP samples. These types of analyses are mainly targeted at making interpretation of the biological data easier. If results for a particular DEEP sample are missing, the author of the respective Process should be contacted and be asked to run the Process to generate the missing results.

Process	Datatype	Description
CSSvX	Histone modifications	Chromatin state segmentation (ChromHMM, EpiCSeg)
RNBvX	DNA methylation	RnBeads analysis
TFAvX	Open chromatin	Transcription factor annotation (TEPIC)

Miscellaneous

The Process documents in the Misc folder are irrelevant for most users. They represent mock-ups to facilitate DAC-internal data management or they describe the conversion steps for DEEP data that are scheduled to be released as IHEC track hubs.