Hi Malcolm, Our engineers have assured me that there isn't an off-by-one error. Since there are two values for the same location in each of these files, you just need select one or the other, which you have done by deleting the line preceding the line with the error.
Please don't hesitate to contact the mail list again if you have any further questions. Katrina Learned UCSC Genome Bioinformatics Group Cook, Malcolm wrote, On 01/14/11 13:02: > Hi Vanessa, > > Thanks for your consideration and open response/confirmation of the issue. > > I have found that deleting a single line from the phastCons file is > sufficient for all 4 occurances of the error in dm3 to go away. > > However, I wonder if there is any guidance regarding exactly which line is in > error. > > I assume most likely it is the first or the last score in a block that should > be removed, but have no menas of confirming. > > It might matter to a subsequent analysis I have planned since I will be > looking at conservation in coding regions as it relates to 'phase' (expecting > more conservation in the wobble position of regulatory regions than that of > non-regulatory coding regions). For this being "off-by-one" in selected > regions would throw off the analysis. > > Sincerely, > > Malcolm Cook > Stowers Institute for Medical Research - Bioinformatics > Kansas City, Missouri USA > > > > >> -----Original Message----- >> From: Vanessa Kirkup Swing [mailto:[email protected]] >> Sent: Friday, January 14, 2011 12:18 PM >> To: Cook, Malcolm >> Cc: Cook, Malcolm; [email protected] >> Subject: Re: [Genome] converting phastCons to bigWig >> >> Dear Malcolm, >> >> Thank you for your patience. Your assumption to remove the >> line from chr2R.pp was correct. The reason you were getting >> the error is because there is a slight overlap. This is a >> known problem with older phastCon files and has been >> corrected with our newer phastCon files. We will put this on >> our long list of things to look into and fix. >> >> If you have further questions, please contact the mailing list. >> >> Vanessa Kirkup Swing >> UCSC Genome Bioinformatics Group >> >> >> ----- Original Message ----- >> From: "Malcolm Cook" <[email protected]> >> To: "Malcolm Cook" <[email protected]>, "[email protected]" >> <[email protected]> >> Sent: Thursday, January 13, 2011 3:35:59 PM >> Subject: Re: [Genome] converting phastCons to bigWig >> >> 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 >> >> > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
