MAINT: readme doc for process files

DEEP · Oct 20, 2016 · 7efa3bd · 7efa3bd
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+# 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