cuffdiff: extract gene info from chr coordinates

[JQL]

Hi,

Cuffdiff output (gene_exp.txt) has chromosome coordinates. What is the quick way to get gene information?

the output has gene names, but some genes don't have gene names. So chromosome coordinates are probably the only way. I didn't think those XLOC IDs are useful for that.

[GenoMax]

If you are working with a genome that is available in Ensembl then using the BioMart tool would be a simple way to get the gene information. http://www.ensembl.org/biomart/martview

You should be able to do something similar with the Table Browser in UCSC genome browser. http://genome.ucsc.edu/cgi-bin/hgTables?command=start

[JQL]

Thank you GenoMax. That works.

Is there a way to do that in batch mode?

If you are working with a genome that is available in Ensembl then using the BioMart tool would be a simple way to get the gene information. http://www.ensembl.org/biomart/martview

You should be able to do something similar with the Table Browser in UCSC genome browser. http://genome.ucsc.edu/cgi-bin/hgTables?command=start

[GenoMax]

Is there a way to do that in batch mode?

You can do BioMart queries through their API. See more info here: http://www.biomart.org/martservice.html