README.md

# DEEP Process Documents


## Standardized pipelines per assay type

Assay | [Alignment](alignment/) | [Quantification](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](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](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.