[TDF currently is still under development, ues it at your own risk.]
Download & Installation
Installation of TDF
You can find the latest distribution of TDF here. Extract the files, go to the TDF folder and use the following command to install the tool:
sudo python setup.py install --rgt-tool=TDF
If you have problems with the installation of TDF, please check here.
Installation of Triplexator
If you have problems installing the Triplexator, please check here.
Configure genome sequence and annotation data
Before performing the test, the genome sequence and annotation data should be configured. Previous installation of wget is required for Mac OS (see complete installation).
cd ~/rgtdata python setupGenomicData.py --mm9 python setupGenomicData.py --hg19
Note that this operation will require a few minutes for completion and will download genome FASTA files.
Example Promoter Test
We will describe the necessary steps to find potential DNA binding domains of FENDRR in the promoter region of genes UP/DOWN regulated after FENDRR siRNA as presented in the TDF publication (to come).
To run TDF with the promoter test, you need as input:
- the FASTA (What is FASTA?)
- the gene list in form of gene symbol or ensembl id
You can download data for executing TDF on FENDRR example here and find two files in FENDRR_mm9 directory:
- FENDRR.fasta: The sequence of FENDRR in FASTA format.
- fendrr_gene_list.txt: A list of genes UP/DOWN regulated after FENDRR siRNA.
Run promoter test
Go to the directory with these files (FENDRR_mm9/). The promoter test can be executed with the following command:
rgt-TDF promotertest -r FENDRR.fasta -de fendrr_gene_list.txt -organism mm9 -rn FENDRR -o promoter_test/FENDRR/
After running the command, all the result files are in the output directory (promoter_test/FENDRR/) with html report: promoter_test/FENDRR/index.html (see result webpage here). Complete usage instructions and more descriptive examples are found here.
Example Genomic Region Test
The genomic region test uses any set of genomic locations as target regions. This test should be used when target DNA regions are indicated by functional studies, such as ChIRP-Seq, CHART-Seq or ChIP-Seq.
Genomic region test requires two files: a RNA sequence in FASTA format and a set of interested genomic regions in BED format.
Before running the test, please make sure you configure the hg19 genome data (here).
We demonstrate the genomic region test with the following files in TERC in hg19 from example data obtained here:
- terc.fasta: RNA sequence of TERC in FASTA format.
- terc_peaks.bed: Target regions of TERC.
- Nregions_hg19.bed: The regions in the genome with “N” letters for masking in randomization.
Run genomic region test
Go to the directory with the files and execute the following command to run the test (it takes about 3~4 hours because 10,000 randomizations is the default):
rgt-TDF regiontest -r terc.fasta -bed terc_peaks.bed -rn TERC -f Nregions_hg19.bed -organism hg19 -o genomic_region_test/TERC
Then all the results and graphics are stored in the output directory (genomic_region_test/TERC) (check example results page here).
Complete usage instructions and more descriptive examples are found in tutorial for genomic region test.
S. Hanzelmann, C.C. Kuo, M. Kalwa, W. Wagner, I. G. Costa, Triplex Domain Finder: Detection of Triple Helix Binding Domains in Long Non-Coding RNAs, biorxiv, 2016 [paper].