The bedGraphToBigWig program was written mostly because wigToBigWig uses so much memory, especially on bedGraphs. To reduce memory use I had to go to a multi-pass design, which makes it unable to sit in a pipe. However if you do have enough memory, you can still use wigToBigWig on bedGraphs, and it will fit in a pipe.
On Mar 23, 2011, at 8:08 AM, Brian Raney wrote: > Malcolm, you're right that the wigToBigWig program will take input > from standard in. The bedGraphToBigWig program will not, as it does a > few passes over the data. > > On Tue, Mar 22, 2011 at 12:52 PM, Cook, Malcolm <[email protected]> wrote: >> word wrap is decidedly not my friend >> >> I hope this is a better formatted counter-example: >> >> curl ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/chr4.pp.gz >> | \ >> gunzip -c | \ >> wigToBigWig -clip stdin <(fetchChromSizes dm3) stdout > \ >> phastCons15way_chr4.bw >> >> bigWigInfo phastCons15way_chr4.bw >> >> >> ~Malcolm >> >> >>> -----Original Message----- >>> From: [email protected] >>> [mailto:[email protected]] On Behalf Of Cook, Malcolm >>> Sent: Tuesday, March 22, 2011 2:22 PM >>> To: 'Brooke Rhead'; 'John Herbert' >>> Cc: '[email protected]' >>> Subject: Re: [Genome] bedGraphToBigWig; reading in from STDIN >>> >>> Brooke, >>> >>> Hmmm.... my mileage varies.... >>> >>> I have found that at least wigToBigWig can stream stdin, as >>> the following example should prove: >>> >>>> curl >>>> >>> ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way/ch >>> r4.pp.gz >>>> | gunzip -c | wigToBigWig -clip stdin <(fetchChromSizes >>> dm3) stdout > >>>> phastCons15way_chr4.bw bigWigInfo phastCons15way_chr4.bw >>> >>> ?? >>> >>> Malcolm Cook >>> Stowers Institute for Medical Research - Bioinformatics >>> Kansas City, Missouri USA >>> >>> >>> >>>> -----Original Message----- >>>> From: [email protected] >>>> [mailto:[email protected]] On Behalf Of Brooke Rhead >>>> Sent: Tuesday, March 22, 2011 1:22 PM >>>> To: John Herbert >>>> Cc: [email protected] >>>> Subject: Re: [Genome] bedGraphToBigWig; reading in from STDIN >>>> >>>> Hi John, >>>> >>>> It is not possible for the *ToBig* utilities to use STDIN >>> and STDOUT, >>>> as they need to do two passes over the file. >>>> >>>> If you have any further questions, please feel free to contact us >>>> again at [email protected]. >>>> >>>> -- >>>> Brooke Rhead >>>> UCSC Genome Bioinformatics Group >>>> >>>> >>>> John Herbert wrote on 3/22/11 7:53 AM: >>>>> Dear UCSC, >>>>> Please can you tell me if it is possible to run the binary >>>> bedGraphToBigWig feeding in from STDIN? >>>>> >>>>> I would like to do something like; ./peaks_to_bedgraph.pl file | >>>> bedGraphToBigWig stdin dm3_sizes output.bigwig (I also make the >>>> assumption that sort command can write to STDOUT). >>>>> >>>>> Any help appreciated and sorry if I missed this option. >>>>> Kind regards, >>>>> >>>>> John. >>>>> _______________________________________________ >>>>> Genome maillist - [email protected] >>>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> _______________________________________________ >>>> Genome maillist - [email protected] >>>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>>> >>> _______________________________________________ >>> Genome maillist - [email protected] >>> https://lists.soe.ucsc.edu/mailman/listinfo/genome >>> >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome >> > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
