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
