diff --git a/Wednesday/ATACflow.md b/Wednesday/ATACflow.md index 04d2a6fa969357d414626ba2b2188d02ce8142f4..91ff7fc8e5296ae4f84f09430ea9c2da4bed07d9 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 +```