Hello Christoph, Thanks for your suggestions. Adding compression to the big* formats is on our radar but the work has not yet been scheduled. Work is underway on browser support for BAM files as custom tracks, and we hope to release that early next year.
Jennfer ------------------------------------------------ Jennifer Jackson UCSC Genome Bioinformatics Group ----- "Christoph Bock" <[email protected]> wrote: > From: "Christoph Bock" <[email protected]> > To: [email protected] > Sent: Saturday, September 26, 2009 6:26:49 PM GMT -08:00 US/Canada Pacific > Subject: [Genome] bigBed/bigWig files excessively large? > > Dear Developers, > > I noticed that *.bigBed files are often 10-fold or even 20-fold larger > than > their more classical *.bed.gz counterparts. Worse still, for *.bigWig > files > a 50-fold bloat is frequently observed. > Such file sizes become a significant problem when hosting thousands > of > high-throughput sequencing datasets for user inspection. It would be > great > if you could provide a solution that enables both (i) selective > upload, and > (ii) reasonable compression. > > The BAM data format [http://samtools.sourceforge.net/SAM1.pdf] > demonstrates > that it is quite possible to combine index-based access with gzip > compression. I'm sure that a similar solution is feasible for > bigBed/bigWig > files as well. Alternatively or in addition, it would be very > convenient if > the UCSC Genome Browser could soon support the SAM/BAM file formats > (which > seem to emerge as the standard data format for large-scale sequencing > data > anyway). > > Thanks, > Christoph > > ___________________________________________________________________ > Dr. Christoph Bock [[email protected]] > Department of Stem Cell and Regenerative Biology > Harvard University > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
