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List of Parameters
renewiegandt edited this page Apr 12, 2019
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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)
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. | - |
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 |
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 |
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 |
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 |
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 |
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". | - |
Parameter | Input | Description | Default |
---|---|---|---|
max_uropa_runs | Integer | Maximum number UROPA runs running parallelized. | 10 |