*To UCSC genome browser and Encode data maintenance team. Hi,
We downloaded HeLa cell line histone data from UCSC Broad Institute Encode Project data. Those were BiGWig files and I simply tried to convert BigWig to Wig file using UCSC program BigWigToWig. However, what I got, actually not Wig format (its look like BED or BEDgraph). I contacted to the Broad institute who submitted these data and they could reproduce this problem. So, they think that it is not the file format they submitted and probably UCSC autority changed the format and they suggested me to communicate UCSC on this issue........... please see the following conversion and problem details....................... hope you can help me to get appropriate data: * ---------- Forwarded message ---------------------------------------------------------------------- From: Noam Shoresh <[email protected]> Date: Mon, Jul 18, 2011 at 8:59 PM Subject: Re: BigWig To: Khademul Islam <[email protected]> Hi Khademul, I did indeed reproduced your results. What's interesting is that the bigwigs that are there are different from the ones that we submitted (of which I have copies), even though they contain the same data: 2:55pm nshoresh@tin ~/Data/Misc $ head test > #bedGraph section chr1:9825-35675 > chr1 9825 9850 0.36 > chr1 9850 9875 1 > chr1 9875 9900 1.2 > chr1 9900 9925 2.64 > chr1 9925 9950 3 > chr1 9950 9975 3 > chr1 9975 10000 3 > chr1 10000 10025 3 > chr1 10025 10050 2.64 > 2:55pm nshoresh@tin ~/Data/Misc $ head test2 > variableStep chrom=chr1 span=25 > 9826 0.36 > 9851 1 > 9876 1.2 > 9901 2.64 > 9926 3 > 9951 3 > 9976 3 > 10001 3 > 10026 2.64 There have been some changes to the bigwig format or the wigtobigwig utilities - and the problem may be related to that. At any rate, it seems like it was the ucsc genome browser people who modified the files, so I suggest you get in touch with them. (It may be simpler for you to write a script to convert the bed to a wig.) Best, Noam ------------------------------------------------------------------------------------------------------------ > On Fri, Jul 15, 2011 at 2:32 PM, Khademul Islam > <[email protected]>wrote: >> >>> Hi Noam, >>> >>> Thanks for your reply. >>> >>> Lets take an example, I tried once again:........... I downloaded >>> following file: >>> >>> http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone >>> >>> wgEncodeBroadHistoneHelas3H3k79me2StdSig.bigWig (*392.5 MB*) >>> >>> HeLa-S3H3K79me2Signal 392 MBbigWig2010-06-21 >>> >>> >>> # by clicking "download" button as I don't see any download link so that >>> I can do "wget" from terminal .................. it is hg19.......... >>> >>> # The I run : (command copy paste from my terminal....) >>> >>> *./bigWigToWig* *wgEncodeBroadHistoneHelas3H3k79me2StdSig.bigWig* * >>> H3k79me2.wig* >>> >>> *head H3k79me2.wig * >>> >>> #bedGraph section chr1:10025-37050 >>> chr1 10025 10050 0.04 >>> chr1 10050 10075 1 >>> chr1 10075 10100 1 >>> chr1 10100 10125 1 >>> chr1 10125 10150 1 >>> chr1 10150 10175 1 >>> >>> >>> >>> ## There is almost no way to run wrong script as I downloaded only this >>> script from UCSC............ >>> ## Also, importantly and surprising, with the same script, when I did a >>> batch run with all my *.BigWig files........ ONLY Broad data BigWig gave me >>> improper Wig file............ other BigWig on hela and Huvec I got from: >>> >>> >>> http://hgdownload.cse.ucsc.edu/goldenPath/hg18/encodeDCC/wgEncodeYaleChIPseq/ >>> >>> http://hgdownload.cse.ucsc.edu/goldenPath/hg19/encodeDCC/wgEncodeUwHistone/ >>> >>> --- gave me proper Wig file. So, I suspect something is wrong in my input >>> file from Broad data. So, could you kindly please check the file size I >>> mentioned should be the same.......and if you download this file from the >>> website by clicking "Download" button (not from your stored file) and then >>> try to convert, it goes fine ? >>> >>> I used following script from UCSC (downloaded 2 day ago): >>> >>> bigWigToWig >>> <http://hgdownload.cse.ucsc.edu/admin/exe/linux.x86_64/bigWigToWig> >>> 05-Jul-2011 18:18 245K >>> >>> >>> >>> Thank you once again, >>> >>> Khademul >>> >>> >>> >>> >>> =========================================================== >>> >>>> >>>> >>>> On Fri, Jul 15, 2011 at 11:24 AM, Khademul Islam < >>>> [email protected]> wrote: >>>> >>>>> Hi Noam Shoresh, >>>>> >>>>> >>>>> I just downloaded Hela Cell Line Histone modification BigWig files from >>>>> : >>>>> >>>>> http://genome.ucsc.edu/cgi-bin/hgFileUi?db=hg19&g=wgEncodeBroadHistone >>>>> >>>>> Basically I wanted Wig file. So, I used UCSC *bigWigToWig* to convert >>>>> the BigWig files. It returned following format for any BiGWig file I >>>>> tried: >>>>> >>>>> #bedGraph ... ..... >>>>> chr1 9925 9950 0.6 >>>>> chr1 9950 9975 1 >>>>> chr1 9975 10000 1.76 >>>>> chr1 10000 10025 2 >>>>> chr1 10025 10050 2 >>>>> chr1 10050 10075 2 >>>>> >>>>> -- but this does not look like proper Wig file. >>>>> >>>>> # However, if I download BiWig files of Hela cell line Histone data >>>>> generated by any other institute.............. and use the same UCSC >>>>> bigWigToWig script to convert, I get proper Wig file. >>>>> >>>>> Would you be kind to explain why I get different output format from >>>>> Broad Institute data............... and how can I get proper Wig file ? >>>>> >>>>> >>>>> thank you, >>>>> >>>>> >>>>> >>>>> Khademul >>>>> >>>>> Barcelona Biomedical Research Park. >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>>> >>>> >>>> >>>> -- >>>> Noam Shoresh >>>> Senior Computational Biologist >>>> Epigenomics group >>>> The Broad Institute >>>> 857-919-0181 >>>> >>>> ==================== >>>> “A week of hard work can sometimes save you an hour of thought.” >>>> (http://www.swc.scipy.org/lec/debugging.html) >>>> >>> >>> >> >> >> -- >> Noam Shoresh >> Senior Computational Biologist >> Epigenomics group >> The Broad Institute >> 857-919-0181 >> >> ==================== >> “A week of hard work can sometimes save you an hour of thought.” >> (http://www.swc.scipy.org/lec/debugging.html) >> > > -- Noam Shoresh Senior Computational Biologist Epigenomics group The Broad Institute 857-919-0181 ==================== “A week of hard work can sometimes save you an hour of thought.” (http://www.swc.scipy.org/lec/debugging.html) _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
