Convert GSuite tracks from primary to preprocessed (Preprocess tracks to prepare them for use in the analysis tools)

This tool is used to preprocess the textual track files referred to by a GSuite file into a indexed, binary format that is needed for efficient analysis by the HyperBrowser analysis tools.

Genome

Preprocessing tracks requires that the specific genome build is selected. If a genome build is defined within the GSuite file, it can still be overridden by the user if another build is selected. If the GSuite file contains no genome, the selection of a genome build is required.

Supported file types

The HyperBrowser preprocessor supports the following file types (name: file suffix):

Point BED: "point.bed"
Category BED: "category.bed"
Valued BED: "bed, valued.bed, marked.bed"
BED: ""
Category GFF: "category.gff, category.gff3"
GFF: "gff, gff3, gtf"
FASTA: "fasta, fas, fa"
HB function: "hbfunction"
target/control bedGraph: "targetcontrol.bedgraph"
bedGraph: "bedgraph"
Microarray: "microarray"
WIG: "wig"
GTrack: "gtrack.gz"
GTrack: "gtrack"
broadPeak: ".broadpeak"
narrowPeak: ".narrowpeak"

Requirements for GSuite input file

Locations: local

File formats: primary

Track types: any

Genome: optional, multiple genomes allowed

Format of GSuite output file

Location: local

File format: preprocessed

Track type: as input file

Format of GSuite error file

The error GSuite file contains references to all track lines that failed in the execution of the tool. This is a valid GSuite file that can be used as input in manipulation tools, if one needs to change the contents somehow, or used directly as a input in the current tool to reexecute it only on the failed tracks.

Location: local

File format: primary

Track type: as input file