Tool Usage

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.