This tool converts files between the following file formats:
GTrack: See the 'Show GTrack specification' tool
BED: BED specification
WIG: WIG specification
bedGraph: bedGraph specification
GFF: GFF version 3 specification
FASTA: bedGraph specification
The input data type is defined by the format field of the history element of the data. The available conversions for the selected format are automatically shown in the conversion selection box
Genome
Some GTrack files require a specified genome to be valid, e.g. if bounding regions are specified without explicit end coordinates.
GTrack subtypes
If the conversion to extended GTrack is selected, GTrack subtype information may be added to the output file. The following GTrack subtypes are automatically detected from the contents of the input file:
Notice
The GFF support is somewhat preliminary. For conversions between BED and GFF, we recommend the specialized Galaxy tools: 'BED-to-GFF converter' and 'GFF-to-BED converter'.
Example 1
Input file (BED)
chrM 71 82 A 1000 + 71 79 0,0,255 2 4,4, 0,8
chrM 103 105 B 800 . 103 105 0,255,0 1 2 0
chr21 3 13 C 645 - 3 13 255,0,0 3 2,2,2 0,5,8
Output file (Extended GTrack)
##gtrack version: 1.0
##track type: valued segments
##uninterrupted data lines: true
###seqid start end value strand name thickstart thickend itemrgb blockcount blocksizes blockstarts
chrM 71 82 1000 + A 71 79 0,0,255 2 4,4, 0,8
chrM 103 105 800 . B 103 105 0,255,0 1 2 0
chr21 3 13 645 - C 3 13 255,0,0 3 2,2,2 0,5,8
Example 2
Input file (WIG)
track type=wiggle_0
fixedStep chrom=chrM start=11 step=10 span=5
4.500
-3.700
fixedStep chrom=chrM start=1013 step=10 span=5
2.100
11.00
fixedStep chrom=chr21 start=201 step=10 span=5
21.10
Output file (bedGraph)
track type=bedGraph
chrM 10 15 4.500
chrM 20 25 -3.700
chrM 1012 1017 2.100
chrM 1022 1027 11.00
chr21 200 205 21.10
Output file (GTrack)
##gtrack version: 1.0
##track type: valued segments
##1-indexed: true
##end inclusive: true
##fixed length: 5
##fixed gap size: 5
##gtrack subtype: wig fixedstep
##subtype url: http://gtrack.no/wig_fixedstep.gtrack
##subtype adherence: strict
###value
####seqid=chrM; start=11; end=25
4.5
-3.7
####seqid=chrM; start=1013; end=1027
2.1
11.0
####seqid=chr21; start=201; end=205
21.1
Example
See full example of how to use this tool.