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 |