Hi Kayla, I was able to convert some wig files into the bigWig format and display the tracks in the UCSC genome browser. However, during the conversion from wig to bigWig format, I noticed that "wigToBigWig" consumes a lot of memory. For example, to convert a ~10 Gb wig file, it maxed out our server with 32 Gb memory and used >10 Gb of swap space as well. This make the conversion runs quite slowly (~10 hr). Do you have any suggestions as to how to make this process more memory efficient?
Thanks! -Wei Kayla Smith <[email protected]> 05/20/2009 04:56 PM To [email protected] cc [email protected] Subject Re: [Genome] wigToBigWig and bedToBigBed Hello Wei, Thank you for your interest in our new bigBed and bigWig formats. While we have not formally released these utilities, we have made them available here: This first cut of the executables is here: http://genome-test.cse.ucsc.edu/admin/exe/linux.x86_64/ with README files such as the following: http://genome-test.cse.ucsc.edu/admin/exe/linux.x86_64/bigBedWigs.txt Please let us know if you experience any difficulties. Kayla Smith UCSC Genome Bioinformatics Group ----- [email protected] wrote: > Hi, > > I am interested in the new bigwig and bigbed formats. Could you please > > point me to the download site of wigToBigWig and bedToBigBed? Thanks a > > lot! > > -Wei Tao, PhD. > Bioinformatics > Agencourt Bioscience > The server made the following annotations > > --------------------------------------------------------------------------------- > > This message contains information that may be privileged or > confidential and is the property of Beckman Coulter, Inc. It is > intended only for the person to whom it is addressed. If you are not > the intended recipient, you are not authorized to read, print, retain, > copy, disseminate, distribute or use this message or any part thereof. > If you receive this message in error, please notify the sender > immediately and delete all copies of this message. > > --------------------------------------------------------------------------------- > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome The server made the following annotations --------------------------------------------------------------------------------- This message contains information that may be privileged or confidential and is the property of Beckman Coulter, Inc. It is intended only for the person to whom it is addressed. If you are not the intended recipient, you are not authorized to read, print, retain, copy, disseminate, distribute or use this message or any part thereof. If you receive this message in error, please notify the sender immediately and delete all copies of this message. --------------------------------------------------------------------------------- _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
