UniBind - UniBind TFBS extraction

Upload your BED file(s)

Note: All input files should provide genomic regions in BED file format corresponding to appropriate species genome versions.

Analysis title or name

E-mail address for notification

BED file (mandatory):

TF list (optional):

Experiment IDs list (optional):

Species:

Collection:

Note An e-mail address is optional and will only be used to send notifications about analysis results.

About UniBind TFBS extraction

The UniBind TFBS extraction tool allows the extraction of TFBSs from the UniBind database within a set of genomic regions of interest provided as a BED file.

Optionally, the tool also allows for the filtering of the results with either a set of transcription factors or experiment IDs. These can be provided as separate files containing one entry per line. Please note that TFs should be provided as gene symbols.

TFBS extraction tool output and example

Output

The output of the extraction tool is a BED file with the TFBSs overlapping with the input regions. When a list of TFs and/or experiment lists is provided, the output file will only contain TFBSs for the TFs/experiments described in the input lists.

Example

As an example of application, we provide example BED, TFs and experiment files in our bitbucket repository. The tool can also be run from its command-line interface with the following command:

extract_TFBSs_bedtools_gzip.sh -i INPUT BED -b GZIPPED BED [-t TFs] [-e EXPERIMENT IDs] [-o OUTPUT DIR]

When running the command-line interface, the output is printed to standard output when no output directory is specified.