README: Fixed typos

README.md

@@ -31,7 +31,7 @@ conda activate masterenv
 
 **Important Notes:**
 1. For conda the channel bioconda needs to be set as highest priority! This is required due to two different packages with the same name in different channels. For the pipeline the package jellyfish from the channel bioconda is needed and **NOT** the jellyfish package from the channel conda-forge!
-2. The paramtere --create_known_tfbs_path and --tfbs_path need the absolute path. If a relative path is given it will not work due to nextflow changing the working directory. This will soon be updated.
+2. The parameters --create_known_tfbs_path and --tfbs_path need an absolute path. If a relative path is given it will not work due to nextflow changing the working directory. This will soon be updated.
 
 
 ## Quick Start
@@ -45,7 +45,7 @@ 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 [absolute path]/demo/known_tfbs/ --organism hg38
 ```
-**Important Note:** In can happen that tfbsscan does not work due to an unknown bug. If this is the case you will see the error message shown in "Known Issues". If this occurs and "fimo" will also throw this error, try following command:
+**Important Note:** It can happen that tfbsscan does not work due to an unknown bug. If this is the case you will see the error message shown in "Known Issues". If the error occurs first try to change the tfbsscan_method to fimo. If it persists try the 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/ --tfbs_path [absolute path]/demo/known_tfbs_chr1_hg38/ --organism hg38
 ```
@@ -66,7 +66,7 @@ Required arguments:
 	--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)
+	--tfbs_path 		Path to directory with output from tfbsscan. If given tfbsscan will be skipped. (Needs absolute path)
 	]
 
 Optional arguments:
@@ -108,7 +108,7 @@ Optional arguments:
 	--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. (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)