From 5cea64cad7453388c8cd1a0b0f34908ab7566152 Mon Sep 17 00:00:00 2001
From: Fanny Wegner <fwegner@imm.uzh.ch>
Date: Thu, 23 Mar 2023 13:13:03 +0100
Subject: [PATCH] Update file assembly_exercise.md
---
exercises/assembly_exercise.md | 10 +++-------
1 file changed, 3 insertions(+), 7 deletions(-)
diff --git a/exercises/assembly_exercise.md b/exercises/assembly_exercise.md
index 97db07c..5dbcf8b 100644
--- a/exercises/assembly_exercise.md
+++ b/exercises/assembly_exercise.md
@@ -57,10 +57,6 @@ cp -r /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_d
```
-
-
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### Running the analysis
In the assembly scripts you need to specify the variables for the input and output data.
@@ -74,6 +70,9 @@ Submit for each platform the respective assembly script.
* In your `data` space, please create a directory called `ngs`. Inside `ngs`, make a directory for each assembly approach, i.e. `nanopore`, `illumina`, `hybrid`.
+The scripts here, include the assembly as well as the annotation step.
+
+
* Copy the following datasets
**Illumina**
@@ -96,9 +95,6 @@ Submit for each platform the respective assembly script.
# copy all scripts
cp /shares/amr.imm.uzh/data/projects/Blockcourse_BIO296/FS2023/Participants_data/nanopore_scripts/*.sh /data/$USER/ngs/nanopore/
-
-
-
```
**Hybrid**
--
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