converter gtf_to_bedgraph_converter.py $input $out_file1 $attribute_name

**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 ------ .. class:: infomark **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