Hello again Yuan, There is a correction - both the 2bit file and the data in /chromosomes has been identified as being soft-masked. This means that both of those data sources and the file bigZips/chromFa.tar.gz all contain the same sequence information, only in different formats.
We are adding information to our README documents to reflect the accurate information and to remove ambiguity. Thank you for your question! Jennifer --------------------------------- Jennifer Jackson UCSC Genome Informatics Group http://genome.ucsc.edu/ On 4/6/10 10:54 AM, Jennifer Jackson wrote: > Hello Yuan, > > The data in hg19/chromosomes/*fa.gz is not masked. It is the sequence > exactly as published by the data source, as described in the README file > in this directory. > > Both hg19/bigZips/chromFa.tar.gz and hg19/bigZips/chromFamasked.tar.gz > are masked, as described in the README file in this directory. > > The file hg19/bigZips/hg19.2bit contains unmasked sequence. It is a > version of what is contained in /chromosomes/*fa.gz, merged into one > file, converted to 2bit format. > > 2bit format explained: > http://genome.ucsc.edu/FAQ/FAQformat.html#format7 > > Hopefully this resolves the content questions, but please let us know if > anything is still unclear, > > Jennifer > > --------------------------------- > Jennifer Jackson > UCSC Genome Informatics Group > http://genome.ucsc.edu/ > > On 4/6/10 7:12 AM, Yuan Hao wrote: >> Dear list, >> >> May I have a question about the human genome assembly 19 available at >> ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/chromosomes/ >> that whether this genome sequence is repeat-masked or not?If masked, >> in which way? I know there is another directory to get the same genome >> sequence (ftp://hgdownload.cse.ucsc.edu/goldenPath/hg19/bigZips/), >> where contains two assemblies differ in the way to mask repeats, i.e. >> chromFa.tar.gz and chromFamasked.tar.gz. I am not sure which one >> corresponds to the genome under /chromosomes directory. Thank you very >> much in advance! >> >> Regards, >> Yuan >> _______________________________________________ >> Genome maillist - [email protected] >> https://lists.soe.ucsc.edu/mailman/listinfo/genome _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
