Update README.md

README.md

@@ -53,38 +53,48 @@ Required arguments:
 	--motif_db	Path to motif-database in MEME-format
 	--config	Path to UROPA configuration file
 	--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: './')
+				 Path can be set as tfbs_path in next run. (Default: './')
 Optional arguments:
+
 	--tfbs_path Path to directory with output from tfbsscan. If given tfbsscan will not be run.
+
 	Footprint extraction:
 	--window_length INT	(Default: 200)
 	--step INT	(Default: 100)
 	--percentage INT	(Default: 0)
+
 	Filter unknown motifs:
 	--min_size_fp INT	(Default: 10)
 	--max_size_fp INT	(Default: 100)
+
 	Clustering:
 	Sequence preparation/ reduction:
 	--kmer INT	Kmer 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.
 	--min_seq_length Interations	Remove all sequences below this value. (Default: 10)
+
 	Clustering:
 	--global INT	Global (=1) or local (=0) alignment. (Default: 0)
 	--identity FLOAT	Identity threshold. (Default: 0.8)
 	--sequence_coverage INT	Minimum aligned nucleotides on both sequences. (Default: 8)
 	--memory INT	Memory limit in MB. 0 for unlimited. (Default: 800)
 	--throw_away_seq INT	Remove all sequences equal or below this length before clustering. (Default: 9)
 	--strand INT	Align +/+ & +/- (= 1). Or align only +/+ (= 0). (Default: 0)
+
 	Motif estimation:
+	--min_seq INT 		Sets the minimum number of sequences required for the FASTA-files given to GLAM2. (Default: 100)
 	--motif_min_len INT	Minimum length of Motif (Default: 8)
 	--motif_max_len INT	Maximum length of Motif (Default: 20)
-	--iteration INT	Number of iterations done by glam2. More Iterations: better results, higher runtime. (Default: 10000)
+	--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)
+
 	Moitf clustering:
+	--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:
 	--organism [hg38 | hg19 | mm9 | mm10]
 	--tissues