thanks, can you please tell me what the format is called? Yu
________________________________ From: Pauline Fujita <[email protected]> To: Yuan Jian <[email protected]> Cc: UCSC <[email protected]> Sent: Friday, 15 June 2012 4:16 AM Subject: Re: [Genome] strand Hello Yu, We don't recommend converting to GFF or using GFF for this purpose. If you are having difficulty lifting negative strand items this won't be fixed by switching to the GFF file format. If you could send us more information about what you are trying to accomplish we might be able to suggest a better approach. Best regards, Pauline Fujita UCSC Genome Bioinformatics Group http://genome.ucsc.edu/ On 6/13/12 5:57 AM, Yuan Jian wrote: > Hello, > I downloaded hg18ToHg19.over.chain to left my bed file. > but I found the chrom location for minus strand region in the file isnot > represented in gff format. > for example, > chain 1322981 chr1 247249719 + 2475290 2488984 chr1 249250621 - 246751494 > 246765188 1650 > the location in hg19 is chr1 249250621 - 246751494 246765188, the number > 246751494 and 246765188 are count from the END of chromosome. > could you please tell me why did not use gff format? and do you have gff > format for hg18ToHg19.over.chain file? > thank, > Yu > _______________________________________________ > Genome maillist - [email protected] > https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
