From 61cac6dd9efbac3155404716d99b042938fffda8 Mon Sep 17 00:00:00 2001
From: Victoire BAILLET <victoire.baillet1@pasteur.fr>
Date: Wed, 4 May 2022 16:04:39 +0200
Subject: [PATCH] Update ATACflow.md
---
Wednesday/ATACflow.md | 8 ++++----
1 file changed, 4 insertions(+), 4 deletions(-)
diff --git a/Wednesday/ATACflow.md b/Wednesday/ATACflow.md
index 04d2a6f..91ff7fc 100644
--- a/Wednesday/ATACflow.md
+++ b/Wednesday/ATACflow.md
@@ -100,7 +100,7 @@ fragment_size_distribution:
bamCoverage:
do: yes
- options: "--outFileFormat bigwig --extendReads --binSize 1 --effectiveGenomeSize 2913022398 --normalizeUsing RPKM"
+ options: "--outFileFormat bigwig --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC"
threads: 4
@@ -129,8 +129,8 @@ macs2_peakcalling:
do : yes
cutoff: 0.01
genomeSize: mm
- extsize : 100
- options: ""
+ extsize : 200
+ options: "--shift -100 --keep-dup all"
```
@@ -169,4 +169,4 @@ adapters:
options: -O 6 -u -50 -U 50
quality: 30
threads: 4
-```
\ No newline at end of file
+```
--
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