From 7efa3bd860a176b35c71d0c0e81496eeab846ced Mon Sep 17 00:00:00 2001
From: Peter Ebert <pebert@mpi-inf.mpg.de>
Date: Thu, 20 Oct 2016 22:24:36 +0200
Subject: [PATCH] MAINT: readme doc for process files

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 docs/process.md | 15 +++++++++++++++
 1 file changed, 15 insertions(+)
 create mode 100644 docs/process.md

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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
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