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/chr4.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
