Hi Malcolm, Thanks for the update - does it seem odd to you that both our examples show that problems occur in the lines preceding a block whose start coordinate is "....00001"? Could this be an 0/1 error in array indexing perhaps? Best Daniel
On Wed, Sep 28, 2011 at 7:40 PM, Cook, Malcolm <[email protected]> wrote: > +1: http://www.mail-archive.com/[email protected]/msg03607.html > > > -----Original Message----- > From: [email protected] [mailto:[email protected]] On > Behalf Of daniel.gaffney > Sent: Wednesday, September 28, 2011 11:01 AM > To: [email protected] > Subject: [Genome] PhyloP off by one errors? > > Hi, > I've been trying to convert the hg18 phyloP scores for placental mammals to > bigWig format and I've come across what look > like numerous off-by-one errors (and others) in the files posted here: > > ftp://hgdownload.cse.ucsc.edu/goldenPath/hg18/phyloP44way/placentalMammals/ > > I've been using wigToBigWig from the UCSC source to do the conversion. I > use the following code: > > zcat $FILE | wigToBigWig -clip stdin chromSizes.txt test.bw > > where FILE is a wig file from the above directory. So far I've found the > following errors: > > There's more than one value for chr1 base 220000001 (in coordinates that > start with 1). > There's more than one value for chr13 base 60000001 (in coordinates that > start with 1). > There's more than one value for chr16 base 20000001 (in coordinates that > start with 1). > There's more than one value for chr2 base 60000001 (in coordinates that > start with 1). > There's more than one value for chr3 base 180000001 (in coordinates that > start with 1). > There's more than one value for chr4 base 110000001 (in coordinates that > start with 1). > There's more than one value for chrY base 20000001 (in coordinates that > start with 1). > > Removing the value line before the wig line e.g.: > > 0.561 <==== delete this line > fixedStep chrom=chr1 start=220000001 step=1 > > seems to fix the problem, but its pretty time-consuming. I hope this is of > use to somebody - but any ideas why its happening? > Best > Daniel > > > > -- > The Wellcome Trust Sanger Institute is operated by Genome Research > Limited, a charity registered in England with number 1021457 and a > company registered in England with number 2742969, whose registered > office is 215 Euston Road, London, NW1 2BE. > > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
