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GTF-to-BEDGraph (version 1.0.0)

What it does

This tool converts data from GTF format to BEDGraph format (scroll down for format description).

Example

The following data in GFF format:

chr22  GeneA  enhancer  10000000  10001000  500      +   .  gene_id "GeneA"; transcript_id "TranscriptAlpha"; FPKM "2.75"; frac "1.000000";
chr22  GeneA  promoter  10010000  10010100  900      +   .  gene_id "GeneA"; transcript_id "TranscriptsAlpha"; FPKM "2.25"; frac "1.000000";

using the attribute name 'FPKM' will be converted to BEDGraph (note that 1 is subtracted from the start coordinate):

chr22   9999999  10001000   2.75
chr22  10009999  10010100   2.25

About formats

GTF format Gene Transfer Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GTF lines have nine tab-separated fields:

1. seqname - Must be a chromosome or scaffold.
2. source - The program that generated this feature.
3. feature - The name of this type of feature. Some examples of standard feature types are "CDS", "start_codon", "stop_codon", and "exon".
4. start - The starting position of the feature in the sequence. The first base is numbered 1.
5. end - The ending position of the feature (inclusive).
6. score - A score between 0 and 1000. If there is no score value, enter ".".
7. strand - Valid entries include '+', '-', or '.' (for don't know/care).
8. frame - If the feature is a coding exon, frame should be a number between 0-2 that represents the reading frame of the first base. If the feature is not a coding exon, the value should be '.'.
9. group - The group field is a list of attributes. Each attribute consists of a type/value pair. Attributes must end in a semi-colon, and be separated from any following attribute by exactly one space. The attribute list must begin with the two mandatory attributes: (i) gene_id value - A globally unique identifier for the genomic source of the sequence and (ii) transcript_id value - A globally unique identifier for the predicted transcript.

BEDGraph format

The bedGraph format is line-oriented. Bedgraph data are preceeded by a track definition line, which adds a number of options for controlling the default display of this track.

For the track definition line, all options are placed in a single line separated by spaces:
track type=bedGraph name=track_label description=center_label
visibility=display_mode color=r,g,b altColor=r,g,b priority=priority autoScale=on|off alwaysZero=on|off gridDefault=on|off maxHeightPixels=max:default:min graphType=bar|points viewLimits=lower:upper yLineMark=real-value yLineOnOff=on|off windowingFunction=maximum|mean|minimum smoothingWindow=off|2-16
The track type is REQUIRED, and must be bedGraph:
type=bedGraph

Following the track definition line are the track data in four column BED format:

chromA  chromStartA  chromEndA  dataValueA
chromB  chromStartB  chromEndB  dataValueB