Commit 61cac6dd authored by Victoire  BAILLET's avatar Victoire BAILLET
Browse files

Update ATACflow.md

parent 1a717582
...@@ -100,7 +100,7 @@ fragment_size_distribution: ...@@ -100,7 +100,7 @@ fragment_size_distribution:
bamCoverage: bamCoverage:
do: yes do: yes
options: "--outFileFormat bigwig --extendReads --binSize 1 --effectiveGenomeSize 2913022398 --normalizeUsing RPKM" options: "--outFileFormat bigwig --binSize 10 --effectiveGenomeSize 2913022398 --normalizeUsing RPGC"
threads: 4 threads: 4
...@@ -129,8 +129,8 @@ macs2_peakcalling: ...@@ -129,8 +129,8 @@ macs2_peakcalling:
do : yes do : yes
cutoff: 0.01 cutoff: 0.01
genomeSize: mm genomeSize: mm
extsize : 100 extsize : 200
options: "" options: "--shift -100 --keep-dup all"
``` ```
...@@ -169,4 +169,4 @@ adapters: ...@@ -169,4 +169,4 @@ adapters:
options: -O 6 -u -50 -U 50 options: -O 6 -u -50 -U 50
quality: 30 quality: 30
threads: 4 threads: 4
``` ```
\ No newline at end of file
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