Hi Danielle, Hiram has suggested a utility that can help remedy the out-of-range data:
bedClip - Remove lines from bed file that refer to off-chromosome places. usage: bedClip input.bed chrom.sizes output.bed options: -verbose=2 - set to get list of lines clipped and why Downloaded pre-compiled from: http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/ or http://hgdownload.cse.ucsc.edu/admin/exe/macOSX.i386/ We all hope that you are doing well! Please feel free to contact the mailing list support team again if you would like more assistance. Warm wishes, Jen UCSC Genome Browser Support On 9/13/10 10:03 AM, Danielle Lemay wrote: > Hello Browser Team, > > I'm unable to load BED files used previously due to the recently added > out-of-range check (Error: chromEnd larger than chrom chr19 size). It > would be very nice if this were a warning, instead of an error. > > Now that I've verified that it's a third party tool generating an > out-of-bounds element, I will need to post-process all of the BED > files created using this tool in the past year, including some I've > already released to a collaborator. I would much rather be able to > ignore a warning. > > Thanks, > Danielle > > ######################################## > Danielle G. Lemay, PhD > Postdoctoral Scholar, Bruce German's Lab > Food Science and Technology Department > University of California at Davis > (530) 297 7688 > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
