Hi Yu, The hg18ToHg19.over.chain file is in "chain format," described here: http://genome.ucsc.edu/goldenPath/help/chain.html
We use it instead of GFF because it is a much more compact representation of long-running pairwise alignments. (Sorry for any confusion in our previous response . . . we thought you were trying to lift gff-formatted data using liftOver.) If you have further questions, please contact us again at [email protected]. -- Brooke Rhead UCSC Genome Bioinformatics Group On 6/15/12 1:31 AM, Yuan Jian wrote: > 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 _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
