DOC: README with info for non-standard and misc files

docs/README.md

@@ -6,10 +6,31 @@
 Assay | Alignment | Quantification | Comment
 -----|:---------:|:------------:|-------
 ChIP-seq | genome | chip-seq | 6 histone modifications plus input control
-DNaseI-seq | genome | dnase-seq | DNaseI hypersensitivity
-NOMe-seq | bisulfite | xxx | Nucleosome occupancy and DNA methylation
-(m)RNA-seq | xxx | xxx | polyA-enriched total RNA-seq (stranded)
-(sn)RNA-seq | xxx | xxx | micro RNA
-(t)RNA-seq | xxx | xxx | ribo-depleted total RNA-seq (stranded)
-RRBS | bisulfite | xxx | Reduced representation bisulfite sequencing
-WGBS | bisulfite | xxx | Whole-genome bisulfite sequencing
+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.