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.