From 1a740c2a1abf6c4f6364cfad56cc01623af3c698 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Sun, 13 Jan 2019 07:46:46 -0500 Subject: [PATCH] Added demo command to README.md --- README.md | 10 +++++++++- 1 file changed, 9 insertions(+), 1 deletion(-) diff --git a/README.md b/README.md index 07bbdd2..0a0b746 100644 --- a/README.md +++ b/README.md @@ -35,6 +35,14 @@ conda activate masterenv ```console nextflow run pipeline.nf --bigwig [BigWig-file] --bed [BED-file] --genome_fasta [FASTA-file] --motif_db [MEME-file] --organism [mm10|mm9|hg19|hg38] ``` + +### Demo run +There are files provided inside ./demo/ for a demo run. +Go to the main directory and run following command: +``` +nextflow run pipeline.nf --bigwig ./demo/buenrostro50k_chr1_fp.bw --bed ./demo/buenrostro50k_chr1_peaks.bed --genome_fasta ./demo/hg38/hg38_chr1.fa --motif_db ./demo/motif_database/jaspar_vertebrates.meme --out ./demo/buenrostro50k_chr1_out/ --create_known_tfbs_path ./demo/known_tfbs_hg38_chr1/ --organism hg38 +``` + ## Parameters For a detailed overview for all parameters follow this [link](https://github.molgen.mpg.de/loosolab/masterJLU2018/wiki/Configuration). ``` @@ -88,7 +96,7 @@ Optional arguments: --tomtom_treshold FLOAT Threshold for similarity score. (Default: 0.01) --best_motif INT Get the best X motifs per cluster. (Default: 3) Moitf clustering: - --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 0) + --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Default: 0) --edge_weight INT Minimum weight of edges in motif-cluster-graph (Default: 5) --motif_similarity_thresh FLOAT Threshold for motif similarity score (Default: 0.00001)