Well i don't really remenber where and when i got the hg19.chrsize but i think it can be my mistake cos' i realised that i have the same problem with .bw from .bam with mm9 mapping... The fact is that yerterday it was not a problem to have the hg19 chromosome M with wrong size 16909 in .bw but it is today. I've decided to download chromInfo.txt.gz for mm9 and hg19 from your server which contains right chrommosome sizes and reformat .bw files from my servers which represents ~450 .bw files so around ~10 hours (not really a problem to correct that). thanks, kevin.
De ： Hiram Clawson Date/heure ： 2012-02-02 17:20:55 A ： Mingfeng Li Cc ： genome; Kevin LEBRIGAND Sujet ： Re: [Genome] bigWig error: chromSize M does not match assembly. We are currently very puzzled of where these odd numbers are coming from. When you convert from wig to bigWig you use a chrom.sizes file obtained from UCSC. Those are the numbers that are placed in your bigWig file. It is not at all clear how the numbers could be off by odd amounts. --Hiram ----- Original Message ----- From: "Mingfeng Li" <[email protected]> To: "Kevin LEBRIGAND" <[email protected]> Cc: "genome" <[email protected]> Sent: Thursday, February 2, 2012 8:04:34 AM Subject: Re: [Genome] bigWig error: chromSize M does not match assembly. I thinks it is due to the mapping error. I am confused this error should be found during the conversion from wig to bigwig. best, Mingfeng On Thu, Feb 2, 2012 at 5:37 AM, Kevin LEBRIGAND <[email protected]>wrote: > Hi, > Since yesterday, all my hg19 bigwig files give me this error: > Error bigWig data does not match assembly (hg19) - chromSize for chrM in > bigWig (16909) does not match assembly chromSize (16571) > > hg19.chrsize: > ---------------------- > chr1 249250621 > chr2 243199373 > chr3 198022430 > chr4 191154276 > chr5 180915260 > chr6 171115067 > chr7 159138663 > chr8 146364022 > chr9 141213431 > chr10 135534747 > chr11 135006516 > chr12 133851895 > chr13 115169878 > chr14 107349540 > chr15 102531392 > chr16 90354753 > chr17 81195210 > chr18 78077248 > chr19 59128983 > chr20 63025520 > chr21 48129895 > chr22 51304566 > chrX 155270560 > chrY 59373566 > chrM 16909 > ---------------------- > > thanks, > kevin. > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome > -- ********************************************* Mingfeng Li, Ph.D. Postdoctoral Associate Department of Neurobiology Yale University School of Medicine 333 Cedar Street, SHM C-327C New Haven, CT 06510 E-mail: [email protected] Lab: (203) 785-5941 Lab website: www.sestanlab.org ********************************************* _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
