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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 | 1 | 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. By default the length 200 bp was taken as the smallest peak of the test data was 200 bp long. | 200 |
step | Integer | This parameter sets the number of positions to slide the window forward. By default, the step of a length 100 bp was taken. | 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). The user has a possibility to move up or down this threshold using the parameter --percentage. 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. The default percentage is set to 0. | 0 |
min_gap | Integer | This parameter sets the min allowed number of bp in between of two footprints. If there is a smaller number of bp in between of two footprints, the merging of these footprints will be enabled, while 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. ( currently disabled ) | 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 | List/String | List of one or more keywords for tissue-/category-activity, categories must be specified as in JSON config | - |
Parameter | Input | Description | Default |
---|---|---|---|
max_uropa_runs | Integer | Maximum number UROPA runs running parallelized . | 10 |