Dear Hiram, thank you for your quick response and your kind offer to help.
I just noticed in the bigWigInfo output that the latest binary files I obtained from the UCSC website still produce bigWig version 3 files. It seems that might be problematic: https://lists.soe.ucsc.edu/pipermail/genome/2010-October/023674.html I have now built the binaries from source to create bigwig version 4 files instead. The new bigwig files work ! So I guess my problems may have been caused by issues with the bigwig version 3 format. Does that sound reasonable ? Cheers, Thomas Hiram Clawson wrote: > Good Afternoon Thomas: > > This could certainly be a bug in the system. > Can you supply a URL to your bedGraph and chrom.sizes file ? > You can send that to me privately: hiram at soe dot ucsc dot edu > > --Hiram > > Thomas Sandmann wrote: >> Dear UCSC genome browser team, >> >> I am working with a large bedGraph file (800 Mb), which I would like >> to convert to bigWig format for display in a local browser. The data >> is from a non-model organism with a large number of supercontigs as >> chromosomes (>40.000). Unfortunately, when I try to extract data for >> different chromosomes, I only get results for the first two >> chromsomes (v31.000000, v31.000001) but nothing for any of the other >> chromosomes (see below). >> >> I have performed the following steps in a ubuntu Linux environment, >> using binary files from the UCSC genome browser server >> <http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/> that carry >> the date 14-Dec-2010. _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
