How to convert relative coordinate to aboulate coordinate at genome?

Question

[jack]

Hi all,

I have file that contains following information regarding binding of small RNA into genome. Basically it report the relative start and end of 3'UTR and also binding site of small RNAs in the genome. The coordinate reported here is the relative coordinate and I want to convert these coordinates into i global coordinates at the genome. I was wondering whether can someone help me with this ?

    Transcript.ID Species.ID UTR.start UTR.end bind.start bind.end
1 ENST00000263100.3       9544       142     149       219     231
2 ENST00000263100.3       9598       143     150       219     231
3 ENST00000263100.3       9606       143     150       219     231

[liangjiao.xue]

One GFF/GTF file is needed to get the positions and directions of genes on the genome. The input file shown here is very specific. I doubt there is some existing tool to convert the coordinate directly.

Since R is tagged here, you could read the following link to load the GFF/GTF file into memory. https://stat.ethz.ch/pipermail/bioconductor/2008-October/024669.html

Some scripts are needed to check the directions of genes, and get the start point of each gene. After that, the coordinate could be calculated with the relative numbers as shown here.