To follow up a little myself, I find that deleting a single line from chr2R.pp
Namely, deleting the line immediately preceeding fixedStep chrom=chr2R start=5000001 step=1 namely: 0.997 allows wibToBigWig to complete without error. I suspect there is an off-by-one error upstream Can you confirm? Any suggested workaround? Thanks. _____________________________________________ From: Cook, Malcolm Sent: Thursday, January 13, 2011 3:59 PM To: '[email protected]' Subject: converting phastCons to bigWig I get the above message while attempting to convert into bigwig format the dm3 phastcons scores (as downloaded from ftp://hgdownload.cse.ucsc.edu/goldenPath/dm3/phastCons15way) The error occurs only with chromosomes chr2R, X, 3L, and 3R gunzip -c chr2R.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab dm3_chr2R_phastCons15way.bw There's more than one value for chr2R base 5000001 (in coordinates that start with 1). gunzip -c chr3R.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab dm3_chr3R_phastCons15way.bw There's more than one value for chr3R base 7000001 (in coordinates that start with 1). gunzip -c /chrX.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab dm3_chrX_phastCons15way.bw There's more than one value for chrX base 12000001 (in coordinates that start with 1). gunzip -c chr3L.pp.gz | wigToBigWig -clip stdin dm3_chromeSizes.tab dm3_chr3L_phastCons15way.bw There's more than one value for chr3L base 7000001 (in coordinates that start with 1). I'd appreciate understanding if I am mis-using the tools there are some errors in upstream processes generating the phastCons wig files there are some issues with wigToBigWig other ??? My purpose in this converstion is to provide fast random access to the phastCons scores via subsequent calls to bigWigToWig for a analysis I am developing. If there are other (better) ways of acheiving this, I would be similarly obliged to learn. Thanks, Malcolm Cook Stowers Institute for Medical Research - Bioinformatics Kansas City, Missouri USA _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
