From 5dec102cbd660b8d975b9d59a0954d36095bb66f Mon Sep 17 00:00:00 2001
From: BIOPZ-Gypas Foivos <foivos.gypas@unibas.ch>
Date: Fri, 1 Feb 2019 09:47:35 +0100
Subject: [PATCH] Update README.md

---
 README.md | 25 ++++++++++++++++++++++++-
 1 file changed, 24 insertions(+), 1 deletion(-)

diff --git a/README.md b/README.md
index fd362a4..b907f8a 100644
--- a/README.md
+++ b/README.md
@@ -63,9 +63,32 @@ git clone ssh://git@git.scicore.unibas.ch:2222/AnnotationPipelines/riboseq_pipel
 
 ## Configure pipeline
 
-Go in the snakemake directory
+### Download annotation files
+
+Go in the snakemake directory and create a new annotation directory
 ```
 cd riboseq_pipeline/snakemake
+mkdir annotation
+```
+
+Download an annotation file (e.g. gtf from ENSEMBL) and uncompress it
+```
+wget ftp://ftp.ensembl.org/pub/release-90/gtf/homo_sapiens/Homo_sapiens.GRCh38.90.chr.gtf.gz
+gunzip Homo_sapiens.GRCh38.90.chr.gtf.gz
+```
+
+Download a chromosome sequences file (e.g. soft-masked fasta from ENSEMBL) and uncompress it
+```
+wget ftp://ftp.ensembl.org/pub/release-90/fasta/homo_sapiens/dna/Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
+gunzip Homo_sapiens.GRCh38.dna_sm.primary_assembly.fa.gz
+```
+
+Then download rRNAs (e.g. from RefSeq). For the members of the group you can use the following file:
+```
+cp /scicore/home/zavolan/gypas/projects/resources/human/rRNA/rRNA_joao.fa
 ```
 
+Finally copy or create a file with oligos. For the members of the group you can use the following file:
 ```
+cp /scicore/home/zavolan/gypas/projects/resources/human/rRNA/oligos.txt
+```
\ No newline at end of file
-- 
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