List of Parameters

All parameters can be set via the command line ( e.g. --bigwig /path/to/file ) or in the given configuration files. The files are stored in the config directory. You can also write your own configuration files and inculde them to the nextflow.config. (https://www.nextflow.io/docs/latest/config.html#config-include)

Required parameters

Parameter	Input	Description	Default
bigwig	Path	Path to a bigWig-file with the signal over the peaks of interest.	-
bed	Path	Path to a BED-file with peaks of interest corresponding to bigwig file.	-
genome_fasta	Path	Path to the genome in FASTA-format.	-
motif_db	Path	Path to a MEME-file containing known motifs (e.g. Jaspar Core database).	-
organism	String	Input organism must be hg38/hg19 or mm9/mm10.	-
config	Path	Path to UROPA configuration file.	-
gtf_annotation	Path	Path to gtf annotation file (e.g. ensembl mainChr)	-
out	Path	Output path.	./out/
help	Boolean	Show the help message	0
tfbs_path	Path	Path to directory with tfbsscan output. If given tfbsscan will be skipped.	-
gtf_merged	Path	Path to gtf-file for uropa annotation. If a path is set the process is skipped, which creates a gtf-file from the annotation gtf and the gtf containing regulatory elements.	-

Footprint extraction

Parameter	Input	Description	Default
window_length	Integer	This parameter sets the length of a sliding window.	200
step	Integer	This parameter sets the number of positions to slide the window forward.	100
percentage	Integer	By default each signal from the bigWig-file is compared to the threshold which is the mean of signals within a window (or within a peak if this peak is smaller than the chosen window_length). For example --percentage 10 will add 10% of the found threshold within a window and set it as a new threshold to compare the signal to.	0
min_gap	Integer	This parameter sets the minimum number of bp between two footprints. If there is a smaller number of bp between two footprints, these footprints will be merged. The new score is calculated as the mean of scores of both footprints.	6

Filter motifs

Parameter	Input	Description	Default
min	integer	Minimum sequence length threshold. Smaller sequences are discarded.	10
max	integer	Maximum sequence length threshold. discards all sequences longer than this value.	80
tfbsscan_method	moods or fimo	Set method for tfbsscan	moods

Cluster

Parameter	Input	Description	Default
kmer	Integer	k-mer length	10
aprox_motif_length	Integer	Approximate motif length.	10
motif_occurrence	Double	Motif occurrence over all sequences in percent. 0.5 for one motif every two sequences.	1
min_seq_length	Integer	Remove sequences below this length before reduction.	10
global	Integer	Use global (= 1) or local (= 0) sequence identity.	0
identity	Double	Minimum identity between sequences to be added to same cluster.	0.8
sequence_coverage	Integer	Minimum number of aligned nucleotides between to sequences.	8
memory	Integer	Memory limit in MB. (0 for unlimited)	800
throw_away_seq	Integer	Remove sequences with this length and below before clustering.	9
strand	Integer	Do +/+ and +/- alignments during clustering (= 1) or only +/+ (= 0).	0

Motif estimation

Parameter	Input	Description	Default
min_seq	Integer	Sets the minimum number of sequences required for the FASTA-files given to GLAM2	100
motif_min_key	Integer	This parameter is equivalent to the -a parameter of GLAM2. It specifies the minimum number of key positions (aligned columns) in the alignment done by GLAM2.	8
motif_max_key	Integer	This parameter is equivalent to the -b parameter of GLAM2. It specifies the maximum number of key positions (aligned columns) in the alignment done by GLAM2.	20
iteration	Integer	This parameter is equivalent to the -n parameter of GLAM2. It specifies how many iterations should pass since the highest-scoring alignment seen so far before ending each alignment run. The higher the value is the better are the results and the higher is the runtime.	10000
tomtom_treshold	Float	This parameter is equivalent to the -thresh parameter of Tomtom. Tomtom only reports matches with significance values ≤ the set threshold. All clusters with a match are sorted out.	0.01
seed	String	Set a seed for the GLAM2 run.	123456789
best_motif	1-10	Get best X motifs.	3

Motif clustering (available soon)

Parameter	Input	Description	Default
cluster_motif	Boolean	If 1 pipeline clusters motifs. If it's 0 it does not.	0
edge_weight	Integer	Minimum weight of edges in motif-cluster-graph. If the weight is set very high, more and smaller motif clusters are created.	50
motif_similarity_thresh	Float	Threshold for motif similarity score. (See tomtom_treshold)	0.00001

Creating GTF

Parameter	Input	Description	Default
tissue	String	List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON config. The list needs to be whitespace separated. For example: "Aorta Monocyte T-Cell".	-

Evaluation

Parameter	Input	Description	Default
max_uropa_runs	Integer	Maximum number UROPA runs running parallelized.	10