From 89ae0576e7ecd3d61f99e36c96f433189aecb1d4 Mon Sep 17 00:00:00 2001 From: renewiegandt <rene.wiegandt@mpi-bn.mpg.de> Date: Tue, 26 Mar 2019 14:10:27 +0100 Subject: [PATCH] Update parameters in README --- README.md | 11 +++++++---- 1 file changed, 7 insertions(+), 4 deletions(-) diff --git a/README.md b/README.md index d080783..3c6e740 100644 --- a/README.md +++ b/README.md @@ -54,14 +54,14 @@ Required arguments: --genome_fasta Path to genome in FASTA-format --motif_db Path to motif-database in MEME-format --config Path to UROPA configuration file - --organism Input organism [hg38 | hg19 | mm9 | mm10] + --organism Input organism [hg38 | hg19 | mm9 | mm10] --out Output Directory (Default: './out/') Optional arguments: --help [0|1] 1 to show this help message. (Default: 0) --gtf_path Path to gtf-file. If path is set the process which creates a gtf-file is skipped. - --tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will be skipped. + --tfbs_path Path to directory with tfbsscan output. If given tfbsscan will be skipped. Footprint extraction: --window_length INT This parameter sets the length of a sliding window. (Default: 200) @@ -78,7 +78,7 @@ Optional arguments: Sequence preparation/ reduction: --kmer INT K-mer length (Default: 10) --aprox_motif_len INT Motif length (Default: 10) - --motif_occurence FLOAT Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif. + --motif_occurrence FLOAT Percentage of motifs over all sequences. Use 1 (Default) to assume every sequence contains a motif. --min_seq_length Interations Remove all sequences below this value. (Default: 10) Clustering: --global INT Global (=1) or local (=0) alignment. (Default: 0) @@ -96,14 +96,17 @@ Optional arguments: --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) + --seed Set seed for GLAM2 (Default: 123456789) 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) Creating GTF: --tissues List/String List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON config + Evaluation: + --max_uropa_runs INT Maximum number UROPA runs running parallelized (Default: 10) All arguments can be set in the configuration files ```