Hi Skirmantas, I've cc'd this to the Bioc mailing list; hope you don't mind. IGB cannot handle bigWig yet (we are working on it), so bedGraph is your best option. The error below is a bug, but your code would eventually fail, because I'm guessing there is no "genome" entry (e.g., hg19) in the metadata on that object. Without that, or the genome argument or seqlengths argument, BigWig export is not possible (it requires the chromosome lengths). In this case, the seqlengths are probably just the elementLengths of your SimpleRleList (as long as you gave them to the coverage method). Michael On Thu, Apr 28, 2011 at 8:09 AM, Skirmantas Kriaucionis < skirmantas.kriaucionis@ludwig.ox.ac.uk> wrote: > Dear Michael, > > > > After recent upgrade I am having a problem to export SimpleRleList object > which is generated by “coverage” to wig. I get > > > > Error in FUN(X[i], ...) : > > The span must be uniform for Wiggle export. Consider bedGraph or bigWig > as alternatives. > > > > BigWig could probably do (I have to see how IGB handles it), but I get an > error as well: > > > > Error in is.null(genome) : 'genome' is missing > > > > Do you have any advice? > > My data file looks like this: > > > > SimpleRleList of length 21 > > $chr1 > > 'integer' Rle of length 197195432 with 1276791 runs > > Lengths: 3000568 67 37 336 ... 2354 440 6008 > 226 > > Values : 0 1 2 3 ... 0 1 > 0 1 > > > > $chr2 > > 'integer' Rle of length 181748087 with 1518743 runs > > Lengths: 3001054 440 4523 440 ... 1 79 > 4 2 > > Values : 0 1 0 1 ... 24 22 21 > 20 > > > > $chr3 > > 'integer' Rle of length 159599783 with 947316 runs > > Lengths: 3001016 24 416 24 ... 440 2135 440 > 504 > > Values : 0 1 2 1 ... 1 0 > 1 0 > > > > $chr4 > > 'integer' Rle of length 155630120 with 1361168 runs > > Lengths: 3002410 440 3481 270 ... 110 72 13 > 16 > > Values : 0 1 0 1 ... 5 4 > 3 2 > > > > $chr5 > > 'integer' Rle of length 152537259 with 1458847 runs > > Lengths: 3002270 24 51 365 ... 50 464 440 > 62 > > Values : 0 1 2 3 ... 1 0 > 1 0 > > > > ... > > <16 more elements> > > > > Best wishes, > > Skirmantas K. > > > > Skirmantas Kriaucionis, phD > > Ludwig Institute for Cancer Research LTD > > Nuffield Department of Clinical Medicine > > University of Oxford > > Old Road Campus Research Building > > Roosevelt Drive > > Oxford OX3 7DQ > > UK > > > > Tel +44 (0)1865 617536 > > Fax +44 (0)1865 617542 > > > [[alternative HTML version deleted]]