Hi Hiram, In that case, is using chromFaMasked.tar.gz more straightforward? What is the difference between chromFaMasked.tar.gz and the fasta file converted from mm9.2bit?
On Tue, Mar 29, 2011 at 10:03 AM, Hiram Clawson <[email protected]> wrote: > Please use the twoBitToFa program to extract sequence from .2bit files. > > --Hiram > > ----- Original Message ----- > From: "Peng Yu" <[email protected]> > To: "Hiram Clawson" <[email protected]> > Cc: [email protected] > Sent: Tuesday, March 29, 2011 6:38:36 AM > Subject: Re: [Genome] Perl Bio::Das download of repeatmasked sequences? > > Hi Hiram, > > I know that uscs browser source code should have a parer to this type > of files (which is in C (according to the accompany header file), > right?). Is there a library as simple as Bio::DAS that I can call from > scripting language like perl or python without having to know the > details of .2bit file format? > > http://www.perlmonks.org/?node_id=672251 > > Converting .2bit to fasta then using bioperl to parse fasta is one > option. But it seems less straightforward. If there is a stand alone > tool, it would be better. > > On Mon, Mar 28, 2011 at 7:33 PM, Hiram Clawson <[email protected]> wrote: >> Please use the .2bit files fetched from hgdownload for >> local access to genome sequence. >> >> --Hiram >> >> >> On 3/28/11 9:19 AM, Peng Yu wrote: >>> Hi, >>> >>> I'm wondering whether ucsc genome browser DAS has enabled the support >>> repeatmasked sequences. I know that it was not available, but I want >>> to double check if it is available now. >>> >>> https://lists.soe.ucsc.edu/pipermail/genome/2007-March/013165.html >> > > > > -- > Regards, > Peng > -- Regards, Peng _______________________________________________ Genome maillist - [email protected] https://lists.soe.ucsc.edu/mailman/listinfo/genome
