process.md

# DEEP Process Documents


## Standardized pipelines per assay type

Assay | Alignment | Quantification | Comment
-----|:---------:|:------------:|-------
ChIP-seq | genome-aln | chip-seq | 6 histone modifications plus input control
DNaseI-seq | genome-aln | dnase-seq | DNaseI hypersensitivity
NOMe-seq | bisulfite-aln | 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-aln | xxx | Reduced representation bisulfite sequencing
WGBS | bisulfite-aln | xxx | Whole-genome bisulfite sequencing