From 00a5854ec8df9596cd0f264ba8af7e56cc112ad9 Mon Sep 17 00:00:00 2001 From: =?UTF-8?q?Ren=C3=A9=20Wiegandt?= Date: Fri, 18 Jan 2019 17:47:13 -0500 Subject: [PATCH] README: parameter update --- README.md | 14 +++++++++----- 1 file changed, 9 insertions(+), 5 deletions(-) diff --git a/README.md b/README.md index 53cdc16..4cb7b67 100644 --- a/README.md +++ b/README.md @@ -62,14 +62,17 @@ Required arguments: --config Path to UROPA configuration file --organism Input organism [hg38 | hg19 | mm9 | mm10] --out Output Directory (Default: './out/') + [ + --create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored. + Path can be set as tfbs_path in next run. (Needs absolute path) + or + --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. (Needs absolute path) + ] Optional arguments: --help [0|1] 1 to show this help message. (Default: 0) - --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run. - --create_known_tfbs_path Path to directory where output from tfbsscan (known motifs) are stored. - Path can be set as tfbs_path in next run. (Default: './') - --gtf_path Path to gtf-file. If path is set the process which creats a gtf-file is skipped. + --gtf_path Path to gtf-file. If path is set the process which creats a gtf-file is skipped. Footprint extraction: --window_length INT This parameter sets the length of a sliding window. (Default: 200) @@ -103,8 +106,9 @@ Optional arguments: --iteration INT Number of iterations done by GLAM2. More Iterations: better results, higher runtime. (Default: 10000) --tomtom_treshold FLOAT Threshold for similarity score. (Default: 0.01) --best_motif INT Get the best X motifs per cluster. (Default: 3) + --gap_penalty INT Set penalty for gaps in GLAM2 (Default: 1000) Moitf clustering: - --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Default: 0) + --cluster_motif Boolean If 1 pipeline clusters motifs. If its 0 it does not. (Defaul: 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)