TDF includes the following submodes:
- promotertest: Promoter test evaluates the association between the given lncRNA to the target promoters.
- regiontest: Genomic region test evaluates the association between the given lncRNA to the target regions by randomization.
- get_dbss: Get TTSs in BED format from the single BED file
- integrate: Integrate the project’s links and generate project-level statistics.
Here we introduce the common parameters for two main tests (promoter test and genomic region test) first and then describe their test-specific parameters. The last three scripts as the tools are introduced afterward.
Common Inputs for both tests
TDF can be executed with the following command:
rgt-TDF {promotertest,regiontest} [required inputs] [options]
Where:
- {promotertest,regiontest}: Define the applying test, either promoter test, or genomic region test.
- [required inputs]: Required inputs files and paths.
- [options]: Additional input parameters or output options.
There are some inputs common for both tests shown below:
Required Input for both tests
| Option Name | Type | Description |
|---|---|---|
| -h, –help | Show the help message and exit | |
| -r | PATH | Input file name for RNA sequence (in fasta format) |
| -rn | String | Define the RNA name |
| -o | PATH | Output directory name for all the results and temporary files |
| -organism | String | Define the organism (hg19, hg38, mm9, mm10… etc) |
Options
| Option Name | Type | Default | Description |
|---|---|---|---|
| -t | String | RNA name | Define the title name for the results under the Output name. |
| -a | Float | 0.05 | Define significance level for rejection null hypothesis |
| -ccf | Integer | 20 | Define the cut off value for promoter counts |
| -rt | Boolean | False | Remove temporary files (fa, txp…etc) |
| -log | Boolean | False | Set the plots in log scale |
| -ac | PATH | None | Input file for RNA accecibility |
| -accf | Integer | 500 | Define the cut off value for RNA accecibility |
| -obed | Boolean | False | Output the BED files for DNA binding sites. |
| -showpa | Boolean | False | Show parallel and antiparallel bindings in the plot separately. |
| -filter_havana | Boolean | False | Apply filtering to remove HAVANA entries. |
| -protein_coding | Boolean | False | Apply filtering to get only protein coding genes. |
| -known_only | Boolean | False | Apply filtering to get only known genes. |
| -nofile | Boolean | False | Don’t save any files in the output folder, except the statistics. |
Options for TRIPLEXES
The arguments of the TRIPLEXES can be adjusted by the options below.
| Option Name | Type | Default | Description |
|---|---|---|---|
| -l | Integer | 20 | Define the minimum length of triplex |
| -e | Integer | 20 | Set the maximal error-rate in % tolerated |
| -c | Integer | 2 | Sets the tolerated number of consecutive errors with respect to the canonical triplex rules as were found to greatly destabilize triplexes in vitro. |
| -fr | String | off | Activates the filtering of low complexity regions and repeats in the sequence data |
| -fm | Integer | 0 | Method to quickly discard non-hits (Default 0).’0′ = greedy approach; ‘1’ = q-gram filtering. |
| -of | Integer | 1 | Define output formats of Triplexator |
| -mf | Boolean | False | Merge overlapping features into a cluster and report the spanning region. |
| -rm | Boolean | False | Set the multiprocessing |
| -par | String | False | Define other parameters for TRIPLEXES. Please ignore the first “-” and replace space with underline. For example, when you want to add “-G 80 -g 20”, please do “-par G_80_-g_20”. |
Particular Inputs for promoter test
Required Input for promoter test
The target promoters can be defined in two ways:
- A gene list, which contains gene symbols or Ensembl IDs, one gene per line in plain text format. The argument, -de, should be used;
- Two BED files containing the regions of target promoters and non-target promoters (background). Two arguments, -bed and -bg, should be used together.
| Option Name | Type | Description |
|---|---|---|
| -de | PATH | Input file for gene list (gene symbols or Ensembl ID) |
| -bed | PATH | Input BED file of the promoter regions of genes |
| -bg | PATH | Input BED file of the promoter regions of background genes |
Options for promoter test
| Option Name | Type | Default | Description |
|---|---|---|---|
| -pl | Integer | 1000 | Define the promotor length |
| -score | Boolean | False | Load score column from input gene list of BED file for analysis. |
| -scoreh | Boolean | False | Use the header of scores from the given gene list or BED file. |
Particular Inputs for region set test
Required Input for region set test
| Option Name | Type | Description |
|---|---|---|
| -bed | PATH | Input BED file for interesting regions on DNA |
Options for region set test
-mp Integer 0Define the number of threads for multiprocessing.
| Option Name | Type | Default | Description |
|---|---|---|---|
| -n | Integer | 10000 | Number iterations (randomization) |
| -f | PATH | None | Input BED file as mask for randomization |
| -score | Boolean | False | Load score column from input BED file |
get_ttss
Get TTSs of the given RNA sequence with the single BED file.
rgt-TDF get_ttss [options]
| Option Name | Type | Default | Description |
|---|---|---|---|
| -h, –help | show this help message and exit | ||
| -i | PATH | Input BED file of the target regions | |
| -tts | PATH | Output BED file of the TTSs | |
| -tfo | PATH | Output BED file of the TFOs | |
| -tfo | PATH | Output BED file of the TFOs | |
| -r | PATH | Input FASTA file of the RNA | |
| -organism | PATH | Define the organism | |
| -l | Integer | 20 | [Triplexes] Define the minimum length of triplex |
| -e | Integer | 20 | [Triplexes] Set the maximal error-rate in % tolerated |
| -c | Integer | 2 | [Triplexes] Sets the tolerated number of consecutive errors with respect to the canonical triplex rules as such were found to greatly destabilize triplexes in vitro |
| -fr | on/off | off | [Triplexes] Activates the filtering of low complexity regions and repeats in the sequence data |
| -fm | Integer | 0 | [Triplexes] Method to quickly discard non-hits (default: 0).’0′ = greedy approach; ‘1’ = q-gram filtering. |
| -of | Integer | 1 | [Triplexes] Define output formats of Triplexes |
| -mf | Boolean | False | [Triplexes] Merge overlapping features into a cluster and report the spanning region. |
| -rm | Integer | 1 | [Triplexes] Set the multiprocessing |
integrate
Integrate the project’s links and generate project-level statistics.
rgt-TDF integrate [options]
| Option Name | Type | Default | Description |
|---|---|---|---|
| -h, –help | show this help message and exit | ||
| -path | PATH | Define the path of the project. | |
| -exp | PATH | Include expression score for ranking. |