What it does
This tool converts gene transcript annotation from GTF or GFF or GFF3 to UCSC wiggle 12 column BED format.
Example
The following data in GFF3:
chr1 protein_coding gene 11874 14409 0 + . ID=Gene:uc001aaa.3;Name=Gene:uc001aaa.3 chr1 protein_coding transcript 11874 14409 0 + . ID=uc001aaa.3;Name=uc001aaa.3;Parent=Gene:uc001aaa.3 chr1 protein_coding exon 11874 12227 0 + . Parent=uc001aaa.3 chr1 protein_coding exon 12613 12721 0 + . Parent=uc001aaa.3 chr1 protein_coding exon 13221 14409 0 + . Parent=uc001aaa.3
Will be converted to UCSC Wiggle BED format:
chr1 11874 14409 uc001aaa.3 0 + 11874 14409 0 3 354,109,1189, 0,739,1347,
Reference
GFF-to-BED is part of oqtans package and cited as [1].
[1] | Sreedharan VT, Schultheiss SJ, Jean G et.al., Oqtans: the RNA-seq workbench in the cloud for complete and reproducible quantitative transcriptome analysis. Bioinformatics (2014). 10.1093/bioinformatics/btt731 |
About file formats
GFF format General Feature Format is a format for describing genes and other features associated with DNA, RNA and Protein sequences. GFF lines have nine tab-separated fields:
1. seqid - Must be a chromosome or scaffold or contig. 2. source - The program that generated this feature. 3. type - The name of this type of feature. Some examples of standard feature types are "gene", "CDS", "protein", "mRNA", and "exon". 4. start - The starting position of the feature in the sequence. The first base is numbered 1. 5. stop - 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. phase - 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. attributes - All lines with the same group are linked together into a single item.
BED format Browser Extensible Data format was designed at UCSC for displaying data tracks in the Genome Browser. It has three required fields and several additional optional ones:
The first three BED fields (required) are:
1. chrom - The name of the chromosome (e.g. chr1, chrY_random). 2. chromStart - The starting position in the chromosome. (The first base in a chromosome is numbered 0.) 3. chromEnd - The ending position in the chromosome, plus 1 (i.e., a half-open interval).
The additional BED fields (optional) are:
4. name - The name of the BED line. 5. score - A score between 0 and 1000. 6. strand - Defines the strand - either '+' or '-'. 7. thickStart - The starting position where the feature is drawn thickly at the Genome Browser. 8. thickEnd - The ending position where the feature is drawn thickly at the Genome Browser. 9. reserved - This should always be set to zero. 10. blockCount - The number of blocks (exons) in the BED line. 11. blockSizes - A comma-separated list of the block sizes. The number of items in this list should correspond to blockCount. 12. blockStarts - A comma-separated list of block starts. All of the blockStart positions should be calculated relative to chromStart. The number of items in this list should correspond to blockCount.
Copyright
GFF-to-BED Wrapper Version 0.6 (Apr 2015)
2009-2015 Max Planck Society, University of Tübingen & Memorial Sloan Kettering Cancer Center