+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
