In order for any track to be analyzed by The Genomic Hyperbrowser, it needs to be preprocessed into a highly efficient
file format. A track in the preprocessed format is not, however, easily readable and editable by users.
The Extract track tool easily extracts any datasets that are loaded into the system and presents it to the user
as a history element, using either the original file format of the track, or a standard format.
Genome build
Choose the Genome build for the track you want to extract. The track list will update accordingly
Track
Select the track that you want to extract. The tool will not proceed until you have choosen a valid track.
Extract options
Define which regions of the track you want to extract. There are several options:
Bounding regions: The bounding regions of the selected track, if defined
Chromosomes: Any or all complete chromosomes of the genome
Chromosome arms: Any or all complete chromosome arms (excluding centromers) of the genome
Cytobands: Any or all complete cytobands of the genome
Genes (Ensembl): Any or all Ensembl genes in the genome
Custom specification: Any consecutive region of the genome, divided into equal-sized bins
Bins from history: Use the regions defined in a history element (either BED or wig-format)
All options may not be available for all genomes or tracks
N.B. Any segment that is partly inside one of the regions selected is included in the extraction.
To extract all contents of a track, leave the extract options in their default setting (all chromosomes).
Extraction format
Select the track type and file format of the exported track. This list is dynamically created
containing only the meaningful formats for the specific track that is selected. If the option
Original file format is selected, the track is exportet in its original format
(the format of the original file, before preprocessing). For point and segment tracks, each extraction
option is presented with two variants:
Any overlaps merged: return overlapping elements as a single merged element, if any.
A merged element is defined as one segment that spans from the first to the last base pair of any overlapping elements.
Possibly overlapping: return overlapping elements individually, if any.
Separate file per region
If this is checked, the track is extracted in separate files per region defined. All extract files are then compressed together into one single Zip file.