Tool Usage
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.
General Inputs for both tests
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 or mm9) |
| -genome_path |
PATH |
Define the path of genome FASTA file |
Options
| Option Name |
Type |
Default |
Description |
| -showdbs |
Boolean |
False |
Show the plots and statistics of DBS (DNA Binding sites) |
| -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. |
Options for Triplexator
The arguments of theTriplexator can be adjusted by the options below. The default values in TDF is different than Triplexator itself. For detailed information about these arguments please check Triplexator’s manual.
| Option Name |
Type |
Default |
Description |
| -l |
Integer |
15 |
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 |
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
| 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 |
